diff --git a/code/BLUES.R b/code/BLUES.R index c49717985815a98aea07672d59be56897412d8dd..9597e3c2ac78265cb3aece047de8a6044e86df9c 100644 --- a/code/BLUES.R +++ b/code/BLUES.R @@ -1,6 +1,3 @@ - -###B6 Script Specialized for MPI experiment August-September 2018 by Tom Theeuwen################################### - library(lme4); library(lmerTest); library(pbkrtest) setwd('../data/') data <- na.omit(as.data.frame(read.table("s8.csv", sep = ",", header = TRUE))) diff --git a/code/aggregate_analysis.R b/code/aggregate_analysis.R index d4f8b733a8108a6cee564602f5e98c23db74f16a..98c25d1eb551d2a2a23b7b44d1cd299300fa032b 100644 --- a/code/aggregate_analysis.R +++ b/code/aggregate_analysis.R @@ -47,30 +47,33 @@ library("pheatmap") #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ################################################################################################################################################# -all_coexpression_clusters <-readRDS(file ="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/all_coexpression_clusters.rds") -coex_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/coex_markers_number.rds") -coex_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/coex_markers.rds") -go_all_genes=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/go_all_genes.rds") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -go_GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -go_rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers -coex_GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/GF.rds") -coex_rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/rGF.rds") -go_db=read.table("/mnt/LTR_userdata/faroo002/arabidopsis/AtSNPtile1/GO_database.tbl",header=T,sep="\t") - -#go_coex_overlap=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/go_coex_overlap.rds") -#go_coex_overlap_numbers=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/go_coex_overlap_numbers.rds") -#go_coex_overlap_go_percent=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/go_coex_overlap_go_percent.rds") -#go_coex_overlap_coex_percent=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/go_coex_overlap_coex_percent.rds") -#best_go_coex_overlaps_go_percent=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/best_go_coex_overlaps_go_percent.rds") -#best_go_coex_overlaps_coex_percent=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/best_go_coex_overlaps_coex_percent.rds") -#psii_filtered_coex_similarity_using_go=readRDS("psii_filtered_coex_similarity_using_go.tbl") -#psii_filtered_coex_similarity_using_genes=readRDS("psii_filtered_coex_similarity_using_genes.tbl") -#pla_filtered_coex_similarity_using_go=readRDS("pla_filtered_coex_similarity_using_go.tbl") -#pla_filtered_coex_similarity_using_genes=readRDS("pla_filtered_coex_similarity_using_genes.tbl") + + + all_coexpression_clusters <-readRDS(file ="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/all_coexpression_clusters.rds") + coex_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/coex_markers_number.rds") + coex_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/coex_markers.rds") + go_all_genes=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/go_all_genes.rds") + go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 + go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 + go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 + load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") + go_GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers + go_rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers + coex_GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/GF.rds") + coex_rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/rGF.rds") + go_db=read.table("/mnt/LTR_userdata/faroo002/arabidopsis/AtSNPtile1/GO_database.tbl",header=T,sep="\t") + + #go_coex_overlap=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/go_coex_overlap.rds") + #go_coex_overlap_numbers=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/go_coex_overlap_numbers.rds") + #go_coex_overlap_go_percent=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/go_coex_overlap_go_percent.rds") + #go_coex_overlap_coex_percent=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/go_coex_overlap_coex_percent.rds") + #best_go_coex_overlaps_go_percent=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/best_go_coex_overlaps_go_percent.rds") + #best_go_coex_overlaps_coex_percent=readRDS("/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go_vs_coex/best_go_coex_overlaps_coex_percent.rds") + #psii_filtered_coex_similarity_using_go=readRDS("psii_filtered_coex_similarity_using_go.tbl") + #psii_filtered_coex_similarity_using_genes=readRDS("psii_filtered_coex_similarity_using_genes.tbl") + #pla_filtered_coex_similarity_using_go=readRDS("pla_filtered_coex_similarity_using_go.tbl") + #pla_filtered_coex_similarity_using_genes=readRDS("pla_filtered_coex_similarity_using_genes.tbl") + ################################################################################################################################################# # A L L D A T A ################################################################################################################################################# diff --git a/code/make_coex_features_all.R b/code/make_coex_features_all.R index 4e04ad30f7e29f3a417188c778675330dc128372..d14f07782b82106ef1fc69c94057f2072f0a7462 100644 --- a/code/make_coex_features_all.R +++ b/code/make_coex_features_all.R @@ -1,4 +1,8 @@ -message("start...") +#!/usr/bin/env Rscript +args = commandArgs(trailingOnly=TRUE) + +if (length(args)==0) {rerun=FALSE;}else{rerun=args[1]} +message("start making coex features...") ############################# FUNCTIONS ############################################## trim <- function (x) gsub("^\\s+|\\s+$", "", x) `%not_in%` <- purrr::negate(`%in%`) @@ -12,85 +16,89 @@ setwd("../data/priors/coexpression") library('dplyr') library('qgg') ######################################################################################## -MAC_matrix_with_header=readRDS(file="../../MAC_matrix_with_header.rds") -accessions=readRDS(file="../../accessions.rds") -all_nucl_genes_bed=readRDS(file="../../all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="../../ath_all_new_maf_ldpruned_map.rds") -MAC_df=readRDS(file="../../MAC_df.rds") -W=readRDS(file="../../W.rds") -all_coexpression_clusters <-as.data.frame(read.table(file ="ath_gene_clusters.txt", header=TRUE, sep="",strip.white=TRUE)) -coex_markers_number=readRDS(file="coex_markers_number.rds") #7432 -coex_markers=readRDS(file="coex_markers.rds") #7432 -markerSets=readRDS(file="markerSets.rds") +if(rerun==FALSE) +{ + MAC_matrix_with_header=readRDS(file="../../MAC_matrix_with_header.rds") + accessions=readRDS(file="../../accessions.rds") + all_nucl_genes_bed=readRDS(file="../../all_nucl_genes_bed.rds") + ath_all_new_maf_ldpruned_map=readRDS(file="../../ath_all_new_maf_ldpruned_map.rds") + MAC_df=readRDS(file="../../MAC_df.rds") + W=readRDS(file="../../W.rds") + all_coexpression_clusters <-as.data.frame(read.table(file ="ath_gene_clusters.txt", header=TRUE, sep="",strip.white=TRUE)) + coex_markers_number=readRDS(file="coex_markers_number.rds") #7432 + coex_markers=readRDS(file="coex_markers.rds") #7432 + markerSets=readRDS(file="markerSets.rds") +}else{ #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ ########################################################################################### -message("Retrieving markers for each feature") -if(!exists("coex_markers")) -{ - #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - win=0 - gene_regions=data.frame(all_nucl_genes_bed[,1],all_nucl_genes_bed[,2]-win,all_nucl_genes_bed[,3]+win,all_nucl_genes_bed[,4],all_nucl_genes_bed[,6]) - colnames(gene_regions)=c("chr","gstart","gend","gname","strand") - gene_regions[c(2,3)] <- replace(gene_regions[c(2,3)], gene_regions[c(2,3)] < 0, 0) - - coex_markers<-rep(list(list()),nrow(all_coexpression_clusters)) - names(coex_markers)<-all_coexpression_clusters[,1] + message("Retrieving markers for each feature") + if(!exists("coex_markers")) + { + #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + win=0 + gene_regions=data.frame(all_nucl_genes_bed[,1],all_nucl_genes_bed[,2]-win,all_nucl_genes_bed[,3]+win,all_nucl_genes_bed[,4],all_nucl_genes_bed[,6]) + colnames(gene_regions)=c("chr","gstart","gend","gname","strand") + gene_regions[c(2,3)] <- replace(gene_regions[c(2,3)], gene_regions[c(2,3)] < 0, 0) + + coex_markers<-rep(list(list()),nrow(all_coexpression_clusters)) + names(coex_markers)<-all_coexpression_clusters[,1] + + for(i in c(1:nrow(all_coexpression_clusters))) + {message(paste("cluster# ",i)) + unique_lst_of_tair_ids<- as.vector(unique(unlist(as.list(strsplit(as.character(all_coexpression_clusters[i,3]),","))))) + coexgene_regions= gene_regions %>% filter(gname %in% unique_lst_of_tair_ids) #some genes are missed from the list because they could not be found in the list; so I am omitting them without further investigation of the reasons... + mlst<-list() + for(j in 1:nrow(coexgene_regions)) + { + markers=ath_all_new_maf_ldpruned_map %>% filter(chr==coexgene_regions[j,1] & position >= coexgene_regions[j,2] & position<=coexgene_regions[j,3]) %>% mutate_if(is.factor, as.character) + mlst<-c(mlst,as.list(markers["marker_name"])) + } + coex_markers[i]<-list(unique(unlist(unname(mlst)))) + } + coex_markers_number<-numeric(length=length(coex_markers)) + for(i in c(1:length(coex_markers))) + { + coex_markers_number[i]=length(coex_markers[[i]]) + } + names(coex_markers)<-all_coexpression_clusters[,1] + names(coex_markers_number)<-all_coexpression_clusters[,1] - for(i in c(1:nrow(all_coexpression_clusters))) - {message(paste("cluster# ",i)) - unique_lst_of_tair_ids<- as.vector(unique(unlist(as.list(strsplit(as.character(all_coexpression_clusters[i,3]),","))))) - coexgene_regions= gene_regions %>% filter(gname %in% unique_lst_of_tair_ids) #some genes are missed from the list because they could not be found in the list; so I am omitting them without further investigation of the reasons... - mlst<-list() - for(j in 1:nrow(coexgene_regions)) - { - markers=ath_all_new_maf_ldpruned_map %>% filter(chr==coexgene_regions[j,1] & position >= coexgene_regions[j,2] & position<=coexgene_regions[j,3]) %>% mutate_if(is.factor, as.character) - mlst<-c(mlst,as.list(markers["marker_name"])) - } - coex_markers[i]<-list(unique(unlist(unname(mlst)))) + saveRDS(coex_markers_number,"./coex_markers_number.rds") + saveRDS(coex_markers,"./coex_markers.rds") } - coex_markers_number<-numeric(length=length(coex_markers)) - for(i in c(1:length(coex_markers))) + ########################################################################################### + message("Making Genomic Relationship Matrices...") + if(!exists("rGF")) { - coex_markers_number[i]=length(coex_markers[[i]]) - } - names(coex_markers)<-all_coexpression_clusters[,1] - names(coex_markers_number)<-all_coexpression_clusters[,1] - - saveRDS(coex_markers_number,"./coex_markers_number.rds") - saveRDS(coex_markers,"./coex_markers.rds") -} -########################################################################################### -message("Making Genomic Relationship Matrices...") -if(!exists("rGF")) -{ - markerSets<-list() - for(i in c(1:length(coex_markers))) - { - if(length(coex_markers[[i]])>0) - { - markerSets=c(markerSets,coex_markers[i]) - } - } - setsGF <- lapply(markerSets,function(x){ x[x%in%colnames(W)] }) - rsetsGF <- lapply(markerSets,function(x){ colnames(W)[colnames(W) %not_in% x] }) #remaining markers for each feature + markerSets<-list() + for(i in c(1:length(coex_markers))) + { + if(length(coex_markers[[i]])>0) + { + markerSets=c(markerSets,coex_markers[i]) + } + } + setsGF <- lapply(markerSets,function(x){ x[x%in%colnames(W)] }) + rsetsGF <- lapply(markerSets,function(x){ colnames(W)[colnames(W) %not_in% x] }) #remaining markers for each feature - nsets <- length(setsGF) - nsnps <- sapply(setsGF,length) - - #Make Genomic Relationship Matrix for each feature and its remaining markers. - - GF <- lapply(setsGF, function(x) {grm(W = W[, x])}) - rGF <- lapply(rsetsGF, function(x) {grm(W = W[, x])}) + nsets <- length(setsGF) + nsnps <- sapply(setsGF,length) + + #Make Genomic Relationship Matrix for each feature and its remaining markers. + + GF <- lapply(setsGF, function(x) {grm(W = W[, x])}) + rGF <- lapply(rsetsGF, function(x) {grm(W = W[, x])}) -save(markerSets,"./markerSets.rds") -saveRDS(setsGF,"./setsGF.rds") -saveRDS(rsetsGF,"./rsetsGF.rds") -saveRDS(nsets,"./nsets.rds") -saveRDS(nsnps,"./nsnps.rds") -saveRDS(GF,"./GF.rds") -saveRDS(rGF,"./rGF.rds") + save(markerSets,"./markerSets.rds") + saveRDS(setsGF,"./setsGF.rds") + saveRDS(rsetsGF,"./rsetsGF.rds") + saveRDS(nsets,"./nsets.rds") + saveRDS(nsnps,"./nsnps.rds") + saveRDS(GF,"./GF.rds") + saveRDS(rGF,"./rGF.rds") } ######################################################################################## +message("end of script...")] \ No newline at end of file diff --git a/code/make_dataset.R b/code/make_dataset.R index f8dfb3d0e9a6c128fb09073294cd4a03e73cfccc..442d378fab8b5dcad1b9d202bb005a265e002a19 100644 --- a/code/make_dataset.R +++ b/code/make_dataset.R @@ -1,3 +1,7 @@ +#!/usr/bin/env Rscript +args = commandArgs(trailingOnly=TRUE) + +if (length(args)==0) {rerun=FALSE;}else{rerun=args[1]} ############################# FUNCTIONS ############################################## trim <- function (x) gsub("^\\s+|\\s+$", "", x) `%not_in%` <- purrr::negate(`%in%`) @@ -11,116 +15,120 @@ setwd("../data") library('qgg') library('dplyr') ####################################################################################### -MAC_matrix_with_header=readRDS(file="./MAC_matrix_with_header.rds") -accessions=readRDS(file="./accessions.rds") -all_nucl_genes_bed=readRDS(file="./all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="./ath_all_new_maf_ldpruned_map.rds") -MAC_df=readRDS(file="./MAC_df.rds") -W=readRDS(file="./W.rds") +if(rerun==FALSE) +{ + MAC_matrix_with_header=readRDS(file="./MAC_matrix_with_header.rds") + accessions=readRDS(file="./accessions.rds") + all_nucl_genes_bed=readRDS(file="./all_nucl_genes_bed.rds") + ath_all_new_maf_ldpruned_map=readRDS(file="./ath_all_new_maf_ldpruned_map.rds") + MAC_df=readRDS(file="./MAC_df.rds") + W=readRDS(file="./W.rds") -Pheno=readRDS(file="./Pheno.rds") -geno_pheno=readRDS(file="./geno_pheno.rds") -pheno_df=readRDS(file="./pheno_df.rds") + Pheno=readRDS(file="./Pheno.rds") + geno_pheno=readRDS(file="./geno_pheno.rds") + pheno_df=readRDS(file="./pheno_df.rds") -load(file="./Pheno_pla.Rdata") -load(file="./geno_pheno_pla.Rdata") -load(file="./pheno_df_pla.Rdata") -######################################################################################## -message ("loading the Markers...") -if(!exists("MAC_matrix_with_header")) -{ - MAC_matrix_with_header <-as.data.frame(read.table(file ="MAC_matrix", header=TRUE, sep="",strip.white=TRUE)) - accessions<-MAC_matrix_with_header[,1] - saveRDS(MAC_matrix_with_header,"MAC_matrix_with_header.rds") - saveRDS(accessions,"accessions.rds") + load(file="./Pheno_pla.Rdata") + load(file="./geno_pheno_pla.Rdata") + load(file="./pheno_df_pla.Rdata") +}else{ + ######################################################################################## + message ("loading the Markers...") + if(!exists("MAC_matrix_with_header")) + { + MAC_matrix_with_header <-as.data.frame(read.table(file ="MAC_matrix", header=TRUE, sep="",strip.white=TRUE)) + accessions<-MAC_matrix_with_header[,1] + saveRDS(MAC_matrix_with_header,"MAC_matrix_with_header.rds") + saveRDS(accessions,"accessions.rds") -} -message ("loading the Genes List...") -if(!exists("all_nucl_genes_bed")) -{ - all_nucl_genes_bed <-as.data.frame(read.table(file ="TAIR9_GFF3_only_nucl_genes.bed1", header=FALSE, sep="",strip.white=TRUE)) - colnames(all_nucl_genes_bed)<-c("chr","start","end","name","score","strand") - saveRDS(all_nucl_genes_bed,"all_nucl_genes_bed.rds") + } + message ("loading the Genes List...") + if(!exists("all_nucl_genes_bed")) + { + all_nucl_genes_bed <-as.data.frame(read.table(file ="TAIR9_GFF3_only_nucl_genes.bed1", header=FALSE, sep="",strip.white=TRUE)) + colnames(all_nucl_genes_bed)<-c("chr","start","end","name","score","strand") + saveRDS(all_nucl_genes_bed,"all_nucl_genes_bed.rds") -} -message("loading the markers map") -if(!exists("ath_all_new_maf_ldpruned_map")) -{ - ath_all_new_maf_ldpruned_map <-as.data.frame(read.table(file ="ath_all_new_maf_ldpruned.map", header=FALSE, sep="",strip.white=TRUE)) - colnames(ath_all_new_maf_ldpruned_map)<-c("chr","marker_name","score","position") - saveRDS(ath_all_new_maf_ldpruned_map,"ath_all_new_maf_ldpruned_map.rds") -} -message ("loading the Phenotypes...") -if(!exists("Pheno")) -{ - Pheno <-as.data.frame(read.table(file ="psii_pheno_new.tbl", header=TRUE, sep="",strip.white=TRUE)) - saveRDS(Pheno,"Pheno.rds") -} + } + message("loading the markers map") + if(!exists("ath_all_new_maf_ldpruned_map")) + { + ath_all_new_maf_ldpruned_map <-as.data.frame(read.table(file ="ath_all_new_maf_ldpruned.map", header=FALSE, sep="",strip.white=TRUE)) + colnames(ath_all_new_maf_ldpruned_map)<-c("chr","marker_name","score","position") + saveRDS(ath_all_new_maf_ldpruned_map,"ath_all_new_maf_ldpruned_map.rds") + } + message ("loading the Phenotypes...") + if(!exists("Pheno")) + { + Pheno <-as.data.frame(read.table(file ="psii_pheno_new.tbl", header=TRUE, sep="",strip.white=TRUE)) + saveRDS(Pheno,"Pheno.rds") + } -########################################################################################### -message("Aligning genotype and phenotype data...") -if(!exists("geno_pheno")) -{ - geno_pheno<-left_join(MAC_matrix_with_header,Pheno,by="accession") - saveRDS(geno_pheno,"geno_pheno.rds") -} -if(!exists("MAC_df")) -{ - MAC_df<-geno_pheno[,1:ncol(MAC_matrix_with_header)] - MAC_df<-MAC_df[,-1] #remove accessions column - MAC_df <- data.frame(apply(MAC_df, 2, function(x) as.numeric(as.character(x)))) - rownames(MAC_df) <- accessions - saveRDS(MAC_df,file="MAC_df.rds") -} -if(!exists("pheno_df")) -{ - s<-ncol(MAC_matrix_with_header) + 1 - pheno_df<-geno_pheno[,s:ncol(geno_pheno)] - pheno_df <- data.frame(apply(pheno_df, 2, function(x) as.numeric(as.character(x)))) - rownames(pheno_df) <- accessions - saveRDS(pheno_df,file="pheno_df.rds") -} -########################################################################################### -#Make Centered Scaled Genotypes Matrix -message("Making W matrix...") -if(!exists("W")) -{ - nMinor <- colSums(MAC_df, na.rm=TRUE) - nAlleles <- colSums(!is.na(MAC_df)) - p<-nMinor/(2*nAlleles) - - W=t(MAC_df) - for (i in 1:length(accessions)) - { - W[,i] <- (W[,i]-2*p)/sqrt(2*p*(1-p)) - #isNA <- is.na(W[,i]) - #W[isNA,i] <- 0 - } - W <- t(W) - saveRDS(W,"W.rds") -#----------------------------------------------------------------------- - #Make Genomic Relationship Matrix - G <- grm(W=W) - save(G,"G.Rdata") + ########################################################################################### + message("Aligning genotype and phenotype data...") + if(!exists("geno_pheno")) + { + geno_pheno<-left_join(MAC_matrix_with_header,Pheno,by="accession") + saveRDS(geno_pheno,"geno_pheno.rds") + } + if(!exists("MAC_df")) + { + MAC_df<-geno_pheno[,1:ncol(MAC_matrix_with_header)] + MAC_df<-MAC_df[,-1] #remove accessions column + MAC_df <- data.frame(apply(MAC_df, 2, function(x) as.numeric(as.character(x)))) + rownames(MAC_df) <- accessions + saveRDS(MAC_df,file="MAC_df.rds") + } + if(!exists("pheno_df")) + { + s<-ncol(MAC_matrix_with_header) + 1 + pheno_df<-geno_pheno[,s:ncol(geno_pheno)] + pheno_df <- data.frame(apply(pheno_df, 2, function(x) as.numeric(as.character(x)))) + rownames(pheno_df) <- accessions + saveRDS(pheno_df,file="pheno_df.rds") + } + ########################################################################################### + #Make Centered Scaled Genotypes Matrix + message("Making W matrix...") + if(!exists("W")) + { + nMinor <- colSums(MAC_df, na.rm=TRUE) + nAlleles <- colSums(!is.na(MAC_df)) + p<-nMinor/(2*nAlleles) + + W=t(MAC_df) + for (i in 1:length(accessions)) + { + W[,i] <- (W[,i]-2*p)/sqrt(2*p*(1-p)) + #isNA <- is.na(W[,i]) + #W[isNA,i] <- 0 + } + W <- t(W) + saveRDS(W,"W.rds") + #----------------------------------------------------------------------- + #Make Genomic Relationship Matrix + G <- grm(W=W) + save(G,"G.Rdata") -} -########################################################################################### -if(!exists("Pheno_pla")) -{ - Pheno_pla <-as.data.frame(read.table(file ="pla_blue_means.tbl", header=TRUE, sep="",strip.white=TRUE)) - save(Pheno_pla,file="./Pheno_pla.Rdata") -} -message("Aligning genotype and phenotype data...") -if(!exists("geno_pheno_pla")) -{ - geno_pheno_pla<-left_join(MAC_matrix_with_header,Pheno_pla,by="accession") - save(geno_pheno_pla,file="./geno_pheno_pla.Rdata") -} -if(!exists("pheno_df_pla")) -{ - s<-ncol(MAC_matrix_with_header) + 1 - pheno_df_pla<-geno_pheno_pla[,s:ncol(geno_pheno_pla)] - pheno_df_pla <- data.frame(apply(pheno_df_pla, 2, function(x) as.numeric(as.character(x)))) - rownames(pheno_df_pla) <- accessions - save(pheno_df_pla,file="./pheno_df_pla.Rdata") -} + } + ########################################################################################### + if(!exists("Pheno_pla")) + { + Pheno_pla <-as.data.frame(read.table(file ="pla_blue_means.tbl", header=TRUE, sep="",strip.white=TRUE)) + save(Pheno_pla,file="./Pheno_pla.Rdata") + } + message("Aligning genotype and phenotype data...") + if(!exists("geno_pheno_pla")) + { + geno_pheno_pla<-left_join(MAC_matrix_with_header,Pheno_pla,by="accession") + save(geno_pheno_pla,file="./geno_pheno_pla.Rdata") + } + if(!exists("pheno_df_pla")) + { + s<-ncol(MAC_matrix_with_header) + 1 + pheno_df_pla<-geno_pheno_pla[,s:ncol(geno_pheno_pla)] + pheno_df_pla <- data.frame(apply(pheno_df_pla, 2, function(x) as.numeric(as.character(x)))) + rownames(pheno_df_pla) <- accessions + save(pheno_df_pla,file="./pheno_df_pla.Rdata") + } +} \ No newline at end of file diff --git a/code/make_go_features_all.R b/code/make_go_features_all.R index e7057381cb9ae5c493749df1b496520d09b13524..acec39f3b1545d167666a621df4f3068beda4843 100644 --- a/code/make_go_features_all.R +++ b/code/make_go_features_all.R @@ -1,4 +1,8 @@ -message("start of get_go_features.R...") +#!/usr/bin/env Rscript +args = commandArgs(trailingOnly=TRUE) + +if (length(args)==0) {rerun=FALSE;}else{rerun=args[1]} +message("Making GO based features...") ############################# FUNCTIONS ############################################## trim <- function (x) gsub("^\\s+|\\s+$", "", x) `%not_in%` <- purrr::negate(`%in%`) @@ -28,108 +32,111 @@ library('dplyr') library(GO.db) library(org.At.tair.db) ######################################################################################## -MAC_matrix_with_header=readRDS(file="../../MAC_matrix_with_header.rds") -accessions=readRDS(file="../../accessions.rds") -all_nucl_genes_bed=readRDS(file="../../all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="../../ath_all_new_maf_ldpruned_map.rds") -Pheno=readRDS(file="../../Pheno.rds") -geno_pheno=readRDS(file="../../geno_pheno.rds") -MAC_df=readRDS(file="../../MAC_df.rds") -pheno_df=readRDS(file="../../pheno_df.rds") -W=readRDS(file="../../W.rds") - -go_all_genes_number=readRDS(file="go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="go_all_markers.rds") #7432 -markerSets=readRDS(file="markerSets.rds") #7297 -setsGF=readRDS(file="setsGF.rds") #7297 -rsetsGF=readRDS(file="rsetsGF.rds") #7297 -nsets=readRDS(file="nsets.rds") #7297 -nsnps=readRDS(file="nsnps.rds") #7297 -GF=readRDS(file="GF.rds") #7297 -rGF=readRDS(file="rGF.rds") #7297 -########################################################################################### -message("Retrieving markers for each GO") -if(!exists("go_all_markers")) +if(rerun==FALSE) { - go2alltair <- as.list(org.At.tairGO2ALLTAIRS) - go_all_markers<-rep(list(list()),length(go2alltair)) - names(go_all_markers)<-(names(go2alltair)) - go_all_genes_number<-numeric(length=length(go_all_markers)) - if(length(go2alltair) > 0) - { - for(i in c(1:length(go2alltair))) #Loop through all Go terms - { - message(paste("GO#",i)) - goid=names(go2alltair[i]) - tair_ids=go2alltair[i] - lst_of_genes=list() - for(j in 1:length(tair_ids[[1]])) #Loop through all Tair IDs in a GO term - { - lst_of_genes=c(lst_of_genes,unlist(unname(tair_ids[[1]][j]))) - } - unique_lst_of_tair_ids<- as.vector(unique(unlist(lst_of_genes))) - go_all_genes_number[i]<-length(unique_lst_of_tair_ids) - mlst<-list() - for(j in 1:length(unique_lst_of_tair_ids)) - { - #for each gene find its coordinates and then find all markers in it. then append these markers to corresponding GO feature - chromosome=as.numeric(all_nucl_genes_bed[all_nucl_genes_bed["name"]==unique_lst_of_tair_ids[j]][1]) - startpos=as.numeric(all_nucl_genes_bed[all_nucl_genes_bed["name"]==unique_lst_of_tair_ids[j]][2]) - endpos=as.numeric(all_nucl_genes_bed[all_nucl_genes_bed["name"]==unique_lst_of_tair_ids[j]][3]) - markers=ath_all_new_maf_ldpruned_map %>% filter(chr==chromosome & position >= startpos & position<=endpos) %>% mutate_if(is.factor, as.character) - #print(markers) - mlst<-c(mlst,as.list(markers["marker_name"])) - #print (mlst) - } - go_all_markers[i]<-list(unique(unlist(unname(mlst)))) - } + MAC_matrix_with_header=readRDS(file="../../MAC_matrix_with_header.rds") + accessions=readRDS(file="../../accessions.rds") + all_nucl_genes_bed=readRDS(file="../../all_nucl_genes_bed.rds") + ath_all_new_maf_ldpruned_map=readRDS(file="../../ath_all_new_maf_ldpruned_map.rds") + Pheno=readRDS(file="../../Pheno.rds") + geno_pheno=readRDS(file="../../geno_pheno.rds") + MAC_df=readRDS(file="../../MAC_df.rds") + pheno_df=readRDS(file="../../pheno_df.rds") + W=readRDS(file="../../W.rds") - go_all_markers_number<-numeric(length=length(go_all_markers)) - for(i in c(1:length(go_all_markers))) - { - go_all_markers_number[i]=length(go_all_markers[[i]]) - } - - } - saveRDS(go_all_genes_number,"go_all_genes_number.rds") - saveRDS(go_all_markers_number,"go_all_markers_number.rds") - saveRDS(go_all_markers,"go_all_markers.rds") -} -########################################################################################### -#Make Genomic Relationship Matrix for each feature and its remaining markers -message("Making Genomic Relationship Matrices...") -if(!exists("rGF")) -{ - markerSets<-list() - for(i in c(1:length(go_all_markers))) - { - if(length(go_all_markers[[i]])>0) - { - markerSets=c(markerSets,go_all_markers[i]) - } - } - setsGF <- lapply(markerSets,function(x){ x[x%in%colnames(W)] }) - rsetsGF <- lapply(markerSets,function(x){ colnames(W)[colnames(W) %not_in% x] }) #remaining markers for each feature GO term + go_all_genes_number=readRDS(file="go_all_genes_number.rds") #7432 + go_all_markers_number=readRDS(file="go_all_markers_number.rds") #7432 + go_all_markers=readRDS(file="go_all_markers.rds") #7432 + markerSets=readRDS(file="markerSets.rds") #7297 + setsGF=readRDS(file="setsGF.rds") #7297 + rsetsGF=readRDS(file="rsetsGF.rds") #7297 + nsets=readRDS(file="nsets.rds") #7297 + nsnps=readRDS(file="nsnps.rds") #7297 + GF=readRDS(file="GF.rds") #7297 + rGF=readRDS(file="rGF.rds") #7297 +}else{ + message("Retrieving markers for each GO") + if(!exists("go_all_markers")) + { + go2alltair <- as.list(org.At.tairGO2ALLTAIRS) + go_all_markers<-rep(list(list()),length(go2alltair)) + names(go_all_markers)<-(names(go2alltair)) + go_all_genes_number<-numeric(length=length(go_all_markers)) - nsets <- length(setsGF) - nsnps <- sapply(setsGF,length) + if(length(go2alltair) > 0) + { + for(i in c(1:length(go2alltair))) #Loop through all Go terms + { + message(paste("GO#",i)) + goid=names(go2alltair[i]) + tair_ids=go2alltair[i] + lst_of_genes=list() + for(j in 1:length(tair_ids[[1]])) #Loop through all Tair IDs in a GO term + { + lst_of_genes=c(lst_of_genes,unlist(unname(tair_ids[[1]][j]))) + } + unique_lst_of_tair_ids<- as.vector(unique(unlist(lst_of_genes))) + go_all_genes_number[i]<-length(unique_lst_of_tair_ids) + mlst<-list() + for(j in 1:length(unique_lst_of_tair_ids)) + { + #for each gene find its coordinates and then find all markers in it. then append these markers to corresponding GO feature + chromosome=as.numeric(all_nucl_genes_bed[all_nucl_genes_bed["name"]==unique_lst_of_tair_ids[j]][1]) + startpos=as.numeric(all_nucl_genes_bed[all_nucl_genes_bed["name"]==unique_lst_of_tair_ids[j]][2]) + endpos=as.numeric(all_nucl_genes_bed[all_nucl_genes_bed["name"]==unique_lst_of_tair_ids[j]][3]) + markers=ath_all_new_maf_ldpruned_map %>% filter(chr==chromosome & position >= startpos & position<=endpos) %>% mutate_if(is.factor, as.character) + #print(markers) + mlst<-c(mlst,as.list(markers["marker_name"])) + #print (mlst) + } + go_all_markers[i]<-list(unique(unlist(unname(mlst)))) + } - saveRDS(markerSets,"markerSets.rds") - saveRDS(setsGF,"setsGF.rds") - saveRDS(rsetsGF,"rsetsGF.rds") - saveRDS(nsets,"nsets.rds") - saveRDS(nsnps,"nsnps.rds") - - #Make Genomic Relationship Matrix for each feature and its remaining markers. - GF <- lapply(setsGF, function(x) {grm(W = W[, x])}) - saveRDS(GF,"GF.rds") + go_all_markers_number<-numeric(length=length(go_all_markers)) + for(i in c(1:length(go_all_markers))) + { + go_all_markers_number[i]=length(go_all_markers[[i]]) + } + + } + saveRDS(go_all_genes_number,"go_all_genes_number.rds") + saveRDS(go_all_markers_number,"go_all_markers_number.rds") + saveRDS(go_all_markers,"go_all_markers.rds") + } + ########################################################################################### + #Make Genomic Relationship Matrix for each feature and its remaining markers + message("Making Genomic Relationship Matrices...") + if(!exists("rGF")) + { + markerSets<-list() + for(i in c(1:length(go_all_markers))) + { + if(length(go_all_markers[[i]])>0) + { + markerSets=c(markerSets,go_all_markers[i]) + } + } + setsGF <- lapply(markerSets,function(x){ x[x%in%colnames(W)] }) + rsetsGF <- lapply(markerSets,function(x){ colnames(W)[colnames(W) %not_in% x] }) #remaining markers for each feature GO term - rGF <- lapply(rsetsGF, function(x) {grm(W = W[, x])}) - saveRDS(rGF,"rGF.rds") + nsets <- length(setsGF) + nsnps <- sapply(setsGF,length) -} - -######################################################################################## -message("end of get_go_features.R...") + saveRDS(markerSets,"markerSets.rds") + saveRDS(setsGF,"setsGF.rds") + saveRDS(rsetsGF,"rsetsGF.rds") + saveRDS(nsets,"nsets.rds") + saveRDS(nsnps,"nsnps.rds") + + #Make Genomic Relationship Matrix for each feature and its remaining markers. + GF <- lapply(setsGF, function(x) {grm(W = W[, x])}) + saveRDS(GF,"GF.rds") + + rGF <- lapply(rsetsGF, function(x) {grm(W = W[, x])}) + saveRDS(rGF,"rGF.rds") + + } +} + ######################################################################################## + message("end of script...") diff --git a/code/using_COEX/pla/8fold/combine.R b/code/using_COEX/pla/8fold/combine.R new file mode 100644 index 0000000000000000000000000000000000000000..3dad55a225edf737576c4dedca5e24664b369b74 --- /dev/null +++ b/code/using_COEX/pla/8fold/combine.R @@ -0,0 +1,4869 @@ +################################################################################################################################## +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} +setwd(paste0(wdir,"/",wd)); +################################################################################################################################## +T14_1_gblup_prediction_all_1_1000=readRDS(file="T14_1_gblup_prediction_all_1_1000.rds") +T14_1_gblup_prediction_all_1001_2000=readRDS(file="T14_1_gblup_prediction_all_1001_2000.rds") +T14_1_gblup_prediction_all_2001_3000=readRDS(file="T14_1_gblup_prediction_all_2001_3000.rds") +T14_1_gblup_prediction_all_3001_4000=readRDS(file="T14_1_gblup_prediction_all_3001_4000.rds") +T14_1_gblup_prediction_all_4001_5000=readRDS(file="T14_1_gblup_prediction_all_4001_5000.rds") +T14_1_gblup_prediction_all_5001_6000=readRDS(file="T14_1_gblup_prediction_all_5001_6000.rds") +T14_1_gblup_prediction_all_6001_7000=readRDS(file="T14_1_gblup_prediction_all_6001_7000.rds") +T14_1_gblup_prediction_all_7001_8000=readRDS(file="T14_1_gblup_prediction_all_7001_8000.rds") +T14_1_gblup_prediction_all_8001_9000=readRDS(file="T14_1_gblup_prediction_all_8001_9000.rds") +T14_1_gblup_prediction_all_9001_10000=readRDS(file="T14_1_gblup_prediction_all_9001_10000.rds") +T14_1_gblup_prediction_all_10001_11000=readRDS(file="T14_1_gblup_prediction_all_10001_11000.rds") +T14_1_gblup_prediction_all_11001_12419=readRDS(file="T14_1_gblup_prediction_all_11001_12419.rds") +T14_1_gblup_prediction_all=c(T14_1_gblup_prediction_all_1_1000,T14_1_gblup_prediction_all_1001_2000,T14_1_gblup_prediction_all_2001_3000,T14_1_gblup_prediction_all_3001_4000,T14_1_gblup_prediction_all_4001_5000,T14_1_gblup_prediction_all_5001_6000,T14_1_gblup_prediction_all_6001_7000,T14_1_gblup_prediction_all_7001_8000,T14_1_gblup_prediction_all_8001_9000,T14_1_gblup_prediction_all_9001_10000,T14_1_gblup_prediction_all_10001_11000,T14_1_gblup_prediction_all_11001_12419) + +T14_1_gblup_variances_all_1_1000=readRDS(file="T14_1_gblup_variances_all_1_1000.rds") +T14_1_gblup_variances_all_1001_2000=readRDS(file="T14_1_gblup_variances_all_1001_2000.rds") +T14_1_gblup_variances_all_2001_3000=readRDS(file="T14_1_gblup_variances_all_2001_3000.rds") +T14_1_gblup_variances_all_3001_4000=readRDS(file="T14_1_gblup_variances_all_3001_4000.rds") +T14_1_gblup_variances_all_4001_5000=readRDS(file="T14_1_gblup_variances_all_4001_5000.rds") +T14_1_gblup_variances_all_5001_6000=readRDS(file="T14_1_gblup_variances_all_5001_6000.rds") +T14_1_gblup_variances_all_6001_7000=readRDS(file="T14_1_gblup_variances_all_6001_7000.rds") +T14_1_gblup_variances_all_7001_8000=readRDS(file="T14_1_gblup_variances_all_7001_8000.rds") +T14_1_gblup_variances_all_8001_9000=readRDS(file="T14_1_gblup_variances_all_8001_9000.rds") +T14_1_gblup_variances_all_9001_10000=readRDS(file="T14_1_gblup_variances_all_9001_10000.rds") +T14_1_gblup_variances_all_10001_11000=readRDS(file="T14_1_gblup_variances_all_10001_11000.rds") +T14_1_gblup_variances_all_11001_12419=readRDS(file="T14_1_gblup_variances_all_11001_12419.rds") +T14_1_gblup_variances_all=c(T14_1_gblup_variances_all_1_1000,T14_1_gblup_variances_all_1001_2000,T14_1_gblup_variances_all_2001_3000,T14_1_gblup_variances_all_3001_4000,T14_1_gblup_variances_all_4001_5000,T14_1_gblup_variances_all_5001_6000,T14_1_gblup_variances_all_6001_7000,T14_1_gblup_variances_all_7001_8000,T14_1_gblup_variances_all_8001_9000,T14_1_gblup_variances_all_9001_10000,T14_1_gblup_variances_all_10001_11000,T14_1_gblup_variances_all_11001_12419) + +saveRDS(T14_1_gblup_prediction_all,"T14_1_gblup_prediction_all.rds") +saveRDS(T14_1_gblup_variances_all,"T14_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_1_gfblup_prediction_all_1_1000=readRDS(file="T14_1_gfblup_prediction_all_1_1000.rds") +T14_1_gfblup_prediction_all_1001_2000=readRDS(file="T14_1_gfblup_prediction_all_1001_2000.rds") +T14_1_gfblup_prediction_all_2001_3000=readRDS(file="T14_1_gfblup_prediction_all_2001_3000.rds") +T14_1_gfblup_prediction_all_3001_4000=readRDS(file="T14_1_gfblup_prediction_all_3001_4000.rds") +T14_1_gfblup_prediction_all_4001_5000=readRDS(file="T14_1_gfblup_prediction_all_4001_5000.rds") +T14_1_gfblup_prediction_all_5001_6000=readRDS(file="T14_1_gfblup_prediction_all_5001_6000.rds") +T14_1_gfblup_prediction_all_6001_7000=readRDS(file="T14_1_gfblup_prediction_all_6001_7000.rds") +T14_1_gfblup_prediction_all_7001_8000=readRDS(file="T14_1_gfblup_prediction_all_7001_8000.rds") +T14_1_gfblup_prediction_all_8001_9000=readRDS(file="T14_1_gfblup_prediction_all_8001_9000.rds") +T14_1_gfblup_prediction_all_9001_10000=readRDS(file="T14_1_gfblup_prediction_all_9001_10000.rds") +T14_1_gfblup_prediction_all_10001_11000=readRDS(file="T14_1_gfblup_prediction_all_10001_11000.rds") +T14_1_gfblup_prediction_all_11001_12419=readRDS(file="T14_1_gfblup_prediction_all_11001_12419.rds") + +T14_1_gfblup_variances_all_1_1000=readRDS(file="T14_1_gfblup_variances_all_1_1000.rds") +T14_1_gfblup_variances_all_1001_2000=readRDS(file="T14_1_gfblup_variances_all_1001_2000.rds") +T14_1_gfblup_variances_all_2001_3000=readRDS(file="T14_1_gfblup_variances_all_2001_3000.rds") +T14_1_gfblup_variances_all_3001_4000=readRDS(file="T14_1_gfblup_variances_all_3001_4000.rds") +T14_1_gfblup_variances_all_4001_5000=readRDS(file="T14_1_gfblup_variances_all_4001_5000.rds") +T14_1_gfblup_variances_all_5001_6000=readRDS(file="T14_1_gfblup_variances_all_5001_6000.rds") +T14_1_gfblup_variances_all_6001_7000=readRDS(file="T14_1_gfblup_variances_all_6001_7000.rds") +T14_1_gfblup_variances_all_7001_8000=readRDS(file="T14_1_gfblup_variances_all_7001_8000.rds") +T14_1_gfblup_variances_all_8001_9000=readRDS(file="T14_1_gfblup_variances_all_8001_9000.rds") +T14_1_gfblup_variances_all_9001_10000=readRDS(file="T14_1_gfblup_variances_all_9001_10000.rds") +T14_1_gfblup_variances_all_10001_11000=readRDS(file="T14_1_gfblup_variances_all_10001_11000.rds") +T14_1_gfblup_variances_all_11001_12419=readRDS(file="T14_1_gfblup_variances_all_11001_12419.rds") + +cycles=length(T14_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T14_1_gfblup_variances_all=rep(list(list()),cycles) +T14_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_1_1000[[r]]) + T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_1001_2000[[r]]) + T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_2001_3000[[r]]) + T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_3001_4000[[r]]) + T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_4001_5000[[r]]) + T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_5001_6000[[r]]) + T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_6001_7000[[r]]) + T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_7001_8000[[r]]) + T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_8001_9000[[r]]) + T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_9001_10000[[r]]) + T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_10001_11000[[r]]) + T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_11001_12419[[r]]) + + T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_1_1000[[r]]) + T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_1001_2000[[r]]) + T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_2001_3000[[r]]) + T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_3001_4000[[r]]) + T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_4001_5000[[r]]) + T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_5001_6000[[r]]) + T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_6001_7000[[r]]) + T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_7001_8000[[r]]) + T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_8001_9000[[r]]) + T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_9001_10000[[r]]) + T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_10001_11000[[r]]) + T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T14_1_gfblup_prediction_all,"T14_1_gfblup_prediction_all.rds") +saveRDS(T14_1_gfblup_variances_all,"T14_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_2_gblup_prediction_all_1_1000=readRDS(file="T14_2_gblup_prediction_all_1_1000.rds") +T14_2_gblup_prediction_all_1001_2000=readRDS(file="T14_2_gblup_prediction_all_1001_2000.rds") +T14_2_gblup_prediction_all_2001_3000=readRDS(file="T14_2_gblup_prediction_all_2001_3000.rds") +T14_2_gblup_prediction_all_3001_4000=readRDS(file="T14_2_gblup_prediction_all_3001_4000.rds") +T14_2_gblup_prediction_all_4001_5000=readRDS(file="T14_2_gblup_prediction_all_4001_5000.rds") +T14_2_gblup_prediction_all_5001_6000=readRDS(file="T14_2_gblup_prediction_all_5001_6000.rds") +T14_2_gblup_prediction_all_6001_7000=readRDS(file="T14_2_gblup_prediction_all_6001_7000.rds") +T14_2_gblup_prediction_all_7001_8000=readRDS(file="T14_2_gblup_prediction_all_7001_8000.rds") +T14_2_gblup_prediction_all_8001_9000=readRDS(file="T14_2_gblup_prediction_all_8001_9000.rds") +T14_2_gblup_prediction_all_9001_10000=readRDS(file="T14_2_gblup_prediction_all_9001_10000.rds") +T14_2_gblup_prediction_all_10001_11000=readRDS(file="T14_2_gblup_prediction_all_10001_11000.rds") +T14_2_gblup_prediction_all_11001_12419=readRDS(file="T14_2_gblup_prediction_all_11001_12419.rds") +T14_2_gblup_prediction_all=c(T14_2_gblup_prediction_all_1_1000,T14_2_gblup_prediction_all_1001_2000,T14_2_gblup_prediction_all_2001_3000,T14_2_gblup_prediction_all_3001_4000,T14_2_gblup_prediction_all_4001_5000,T14_2_gblup_prediction_all_5001_6000,T14_2_gblup_prediction_all_6001_7000,T14_2_gblup_prediction_all_7001_8000,T14_2_gblup_prediction_all_8001_9000,T14_2_gblup_prediction_all_9001_10000,T14_2_gblup_prediction_all_10001_11000,T14_2_gblup_prediction_all_11001_12419) + +T14_2_gblup_variances_all_1_1000=readRDS(file="T14_2_gblup_variances_all_1_1000.rds") +T14_2_gblup_variances_all_1001_2000=readRDS(file="T14_2_gblup_variances_all_1001_2000.rds") +T14_2_gblup_variances_all_2001_3000=readRDS(file="T14_2_gblup_variances_all_2001_3000.rds") +T14_2_gblup_variances_all_3001_4000=readRDS(file="T14_2_gblup_variances_all_3001_4000.rds") +T14_2_gblup_variances_all_4001_5000=readRDS(file="T14_2_gblup_variances_all_4001_5000.rds") +T14_2_gblup_variances_all_5001_6000=readRDS(file="T14_2_gblup_variances_all_5001_6000.rds") +T14_2_gblup_variances_all_6001_7000=readRDS(file="T14_2_gblup_variances_all_6001_7000.rds") +T14_2_gblup_variances_all_7001_8000=readRDS(file="T14_2_gblup_variances_all_7001_8000.rds") +T14_2_gblup_variances_all_8001_9000=readRDS(file="T14_2_gblup_variances_all_8001_9000.rds") +T14_2_gblup_variances_all_9001_10000=readRDS(file="T14_2_gblup_variances_all_9001_10000.rds") +T14_2_gblup_variances_all_10001_11000=readRDS(file="T14_2_gblup_variances_all_10001_11000.rds") +T14_2_gblup_variances_all_11001_12419=readRDS(file="T14_2_gblup_variances_all_11001_12419.rds") +T14_2_gblup_variances_all=c(T14_2_gblup_variances_all_1_1000,T14_2_gblup_variances_all_1001_2000,T14_2_gblup_variances_all_2001_3000,T14_2_gblup_variances_all_3001_4000,T14_2_gblup_variances_all_4001_5000,T14_2_gblup_variances_all_5001_6000,T14_2_gblup_variances_all_6001_7000,T14_2_gblup_variances_all_7001_8000,T14_2_gblup_variances_all_8001_9000,T14_2_gblup_variances_all_9001_10000,T14_2_gblup_variances_all_10001_11000,T14_2_gblup_variances_all_11001_12419) + +saveRDS(T14_2_gblup_prediction_all,"T14_2_gblup_prediction_all.rds") +saveRDS(T14_2_gblup_variances_all,"T14_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_2_gfblup_prediction_all_1_1000=readRDS(file="T14_2_gfblup_prediction_all_1_1000.rds") +T14_2_gfblup_prediction_all_1001_2000=readRDS(file="T14_2_gfblup_prediction_all_1001_2000.rds") +T14_2_gfblup_prediction_all_2001_3000=readRDS(file="T14_2_gfblup_prediction_all_2001_3000.rds") +T14_2_gfblup_prediction_all_3001_4000=readRDS(file="T14_2_gfblup_prediction_all_3001_4000.rds") +T14_2_gfblup_prediction_all_4001_5000=readRDS(file="T14_2_gfblup_prediction_all_4001_5000.rds") +T14_2_gfblup_prediction_all_5001_6000=readRDS(file="T14_2_gfblup_prediction_all_5001_6000.rds") +T14_2_gfblup_prediction_all_6001_7000=readRDS(file="T14_2_gfblup_prediction_all_6001_7000.rds") +T14_2_gfblup_prediction_all_7001_8000=readRDS(file="T14_2_gfblup_prediction_all_7001_8000.rds") +T14_2_gfblup_prediction_all_8001_9000=readRDS(file="T14_2_gfblup_prediction_all_8001_9000.rds") +T14_2_gfblup_prediction_all_9001_10000=readRDS(file="T14_2_gfblup_prediction_all_9001_10000.rds") +T14_2_gfblup_prediction_all_10001_11000=readRDS(file="T14_2_gfblup_prediction_all_10001_11000.rds") +T14_2_gfblup_prediction_all_11001_12419=readRDS(file="T14_2_gfblup_prediction_all_11001_12419.rds") + +T14_2_gfblup_variances_all_1_1000=readRDS(file="T14_2_gfblup_variances_all_1_1000.rds") +T14_2_gfblup_variances_all_1001_2000=readRDS(file="T14_2_gfblup_variances_all_1001_2000.rds") +T14_2_gfblup_variances_all_2001_3000=readRDS(file="T14_2_gfblup_variances_all_2001_3000.rds") +T14_2_gfblup_variances_all_3001_4000=readRDS(file="T14_2_gfblup_variances_all_3001_4000.rds") +T14_2_gfblup_variances_all_4001_5000=readRDS(file="T14_2_gfblup_variances_all_4001_5000.rds") +T14_2_gfblup_variances_all_5001_6000=readRDS(file="T14_2_gfblup_variances_all_5001_6000.rds") +T14_2_gfblup_variances_all_6001_7000=readRDS(file="T14_2_gfblup_variances_all_6001_7000.rds") +T14_2_gfblup_variances_all_7001_8000=readRDS(file="T14_2_gfblup_variances_all_7001_8000.rds") +T14_2_gfblup_variances_all_8001_9000=readRDS(file="T14_2_gfblup_variances_all_8001_9000.rds") +T14_2_gfblup_variances_all_9001_10000=readRDS(file="T14_2_gfblup_variances_all_9001_10000.rds") +T14_2_gfblup_variances_all_10001_11000=readRDS(file="T14_2_gfblup_variances_all_10001_11000.rds") +T14_2_gfblup_variances_all_11001_12419=readRDS(file="T14_2_gfblup_variances_all_11001_12419.rds") + +cycles=length(T14_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T14_2_gfblup_variances_all=rep(list(list()),cycles) +T14_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_1_1000[[r]]) + T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_1001_2000[[r]]) + T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_2001_3000[[r]]) + T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_3001_4000[[r]]) + T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_4001_5000[[r]]) + T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_5001_6000[[r]]) + T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_6001_7000[[r]]) + T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_7001_8000[[r]]) + T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_8001_9000[[r]]) + T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_9001_10000[[r]]) + T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_10001_11000[[r]]) + T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_11001_12419[[r]]) + + T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_1_1000[[r]]) + T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_1001_2000[[r]]) + T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_2001_3000[[r]]) + T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_3001_4000[[r]]) + T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_4001_5000[[r]]) + T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_5001_6000[[r]]) + T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_6001_7000[[r]]) + T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_7001_8000[[r]]) + T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_8001_9000[[r]]) + T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_9001_10000[[r]]) + T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_10001_11000[[r]]) + T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T14_2_gfblup_prediction_all,"T14_2_gfblup_prediction_all.rds") +saveRDS(T14_2_gfblup_variances_all,"T14_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_3_gblup_prediction_all_1_1000=readRDS(file="T14_3_gblup_prediction_all_1_1000.rds") +T14_3_gblup_prediction_all_1001_2000=readRDS(file="T14_3_gblup_prediction_all_1001_2000.rds") +T14_3_gblup_prediction_all_2001_3000=readRDS(file="T14_3_gblup_prediction_all_2001_3000.rds") +T14_3_gblup_prediction_all_3001_4000=readRDS(file="T14_3_gblup_prediction_all_3001_4000.rds") +T14_3_gblup_prediction_all_4001_5000=readRDS(file="T14_3_gblup_prediction_all_4001_5000.rds") +T14_3_gblup_prediction_all_5001_6000=readRDS(file="T14_3_gblup_prediction_all_5001_6000.rds") +T14_3_gblup_prediction_all_6001_7000=readRDS(file="T14_3_gblup_prediction_all_6001_7000.rds") +T14_3_gblup_prediction_all_7001_8000=readRDS(file="T14_3_gblup_prediction_all_7001_8000.rds") +T14_3_gblup_prediction_all_8001_9000=readRDS(file="T14_3_gblup_prediction_all_8001_9000.rds") +T14_3_gblup_prediction_all_9001_10000=readRDS(file="T14_3_gblup_prediction_all_9001_10000.rds") +T14_3_gblup_prediction_all_10001_11000=readRDS(file="T14_3_gblup_prediction_all_10001_11000.rds") +T14_3_gblup_prediction_all_11001_12419=readRDS(file="T14_3_gblup_prediction_all_11001_12419.rds") +T14_3_gblup_prediction_all=c(T14_3_gblup_prediction_all_1_1000,T14_3_gblup_prediction_all_1001_2000,T14_3_gblup_prediction_all_2001_3000,T14_3_gblup_prediction_all_3001_4000,T14_3_gblup_prediction_all_4001_5000,T14_3_gblup_prediction_all_5001_6000,T14_3_gblup_prediction_all_6001_7000,T14_3_gblup_prediction_all_7001_8000,T14_3_gblup_prediction_all_8001_9000,T14_3_gblup_prediction_all_9001_10000,T14_3_gblup_prediction_all_10001_11000,T14_3_gblup_prediction_all_11001_12419) + +T14_3_gblup_variances_all_1_1000=readRDS(file="T14_3_gblup_variances_all_1_1000.rds") +T14_3_gblup_variances_all_1001_2000=readRDS(file="T14_3_gblup_variances_all_1001_2000.rds") +T14_3_gblup_variances_all_2001_3000=readRDS(file="T14_3_gblup_variances_all_2001_3000.rds") +T14_3_gblup_variances_all_3001_4000=readRDS(file="T14_3_gblup_variances_all_3001_4000.rds") +T14_3_gblup_variances_all_4001_5000=readRDS(file="T14_3_gblup_variances_all_4001_5000.rds") +T14_3_gblup_variances_all_5001_6000=readRDS(file="T14_3_gblup_variances_all_5001_6000.rds") +T14_3_gblup_variances_all_6001_7000=readRDS(file="T14_3_gblup_variances_all_6001_7000.rds") +T14_3_gblup_variances_all_7001_8000=readRDS(file="T14_3_gblup_variances_all_7001_8000.rds") +T14_3_gblup_variances_all_8001_9000=readRDS(file="T14_3_gblup_variances_all_8001_9000.rds") +T14_3_gblup_variances_all_9001_10000=readRDS(file="T14_3_gblup_variances_all_9001_10000.rds") +T14_3_gblup_variances_all_10001_11000=readRDS(file="T14_3_gblup_variances_all_10001_11000.rds") +T14_3_gblup_variances_all_11001_12419=readRDS(file="T14_3_gblup_variances_all_11001_12419.rds") +T14_3_gblup_variances_all=c(T14_3_gblup_variances_all_1_1000,T14_3_gblup_variances_all_1001_2000,T14_3_gblup_variances_all_2001_3000,T14_3_gblup_variances_all_3001_4000,T14_3_gblup_variances_all_4001_5000,T14_3_gblup_variances_all_5001_6000,T14_3_gblup_variances_all_6001_7000,T14_3_gblup_variances_all_7001_8000,T14_3_gblup_variances_all_8001_9000,T14_3_gblup_variances_all_9001_10000,T14_3_gblup_variances_all_10001_11000,T14_3_gblup_variances_all_11001_12419) + +saveRDS(T14_3_gblup_prediction_all,"T14_3_gblup_prediction_all.rds") +saveRDS(T14_3_gblup_variances_all,"T14_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_3_gfblup_prediction_all_1_1000=readRDS(file="T14_3_gfblup_prediction_all_1_1000.rds") +T14_3_gfblup_prediction_all_1001_2000=readRDS(file="T14_3_gfblup_prediction_all_1001_2000.rds") +T14_3_gfblup_prediction_all_2001_3000=readRDS(file="T14_3_gfblup_prediction_all_2001_3000.rds") +T14_3_gfblup_prediction_all_3001_4000=readRDS(file="T14_3_gfblup_prediction_all_3001_4000.rds") +T14_3_gfblup_prediction_all_4001_5000=readRDS(file="T14_3_gfblup_prediction_all_4001_5000.rds") +T14_3_gfblup_prediction_all_5001_6000=readRDS(file="T14_3_gfblup_prediction_all_5001_6000.rds") +T14_3_gfblup_prediction_all_6001_7000=readRDS(file="T14_3_gfblup_prediction_all_6001_7000.rds") +T14_3_gfblup_prediction_all_7001_8000=readRDS(file="T14_3_gfblup_prediction_all_7001_8000.rds") +T14_3_gfblup_prediction_all_8001_9000=readRDS(file="T14_3_gfblup_prediction_all_8001_9000.rds") +T14_3_gfblup_prediction_all_9001_10000=readRDS(file="T14_3_gfblup_prediction_all_9001_10000.rds") +T14_3_gfblup_prediction_all_10001_11000=readRDS(file="T14_3_gfblup_prediction_all_10001_11000.rds") +T14_3_gfblup_prediction_all_11001_12419=readRDS(file="T14_3_gfblup_prediction_all_11001_12419.rds") + +T14_3_gfblup_variances_all_1_1000=readRDS(file="T14_3_gfblup_variances_all_1_1000.rds") +T14_3_gfblup_variances_all_1001_2000=readRDS(file="T14_3_gfblup_variances_all_1001_2000.rds") +T14_3_gfblup_variances_all_2001_3000=readRDS(file="T14_3_gfblup_variances_all_2001_3000.rds") +T14_3_gfblup_variances_all_3001_4000=readRDS(file="T14_3_gfblup_variances_all_3001_4000.rds") +T14_3_gfblup_variances_all_4001_5000=readRDS(file="T14_3_gfblup_variances_all_4001_5000.rds") +T14_3_gfblup_variances_all_5001_6000=readRDS(file="T14_3_gfblup_variances_all_5001_6000.rds") +T14_3_gfblup_variances_all_6001_7000=readRDS(file="T14_3_gfblup_variances_all_6001_7000.rds") +T14_3_gfblup_variances_all_7001_8000=readRDS(file="T14_3_gfblup_variances_all_7001_8000.rds") +T14_3_gfblup_variances_all_8001_9000=readRDS(file="T14_3_gfblup_variances_all_8001_9000.rds") +T14_3_gfblup_variances_all_9001_10000=readRDS(file="T14_3_gfblup_variances_all_9001_10000.rds") +T14_3_gfblup_variances_all_10001_11000=readRDS(file="T14_3_gfblup_variances_all_10001_11000.rds") +T14_3_gfblup_variances_all_11001_12419=readRDS(file="T14_3_gfblup_variances_all_11001_12419.rds") + +cycles=length(T14_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T14_3_gfblup_variances_all=rep(list(list()),cycles) +T14_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_1_1000[[r]]) + T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_1001_2000[[r]]) + T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_2001_3000[[r]]) + T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_3001_4000[[r]]) + T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_4001_5000[[r]]) + T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_5001_6000[[r]]) + T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_6001_7000[[r]]) + T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_7001_8000[[r]]) + T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_8001_9000[[r]]) + T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_9001_10000[[r]]) + T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_10001_11000[[r]]) + T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_11001_12419[[r]]) + + T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_1_1000[[r]]) + T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_1001_2000[[r]]) + T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_2001_3000[[r]]) + T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_3001_4000[[r]]) + T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_4001_5000[[r]]) + T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_5001_6000[[r]]) + T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_6001_7000[[r]]) + T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_7001_8000[[r]]) + T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_8001_9000[[r]]) + T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_9001_10000[[r]]) + T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_10001_11000[[r]]) + T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T14_3_gfblup_prediction_all,"T14_3_gfblup_prediction_all.rds") +saveRDS(T14_3_gfblup_variances_all,"T14_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_4_gblup_prediction_all_1_1000=readRDS(file="T14_4_gblup_prediction_all_1_1000.rds") +T14_4_gblup_prediction_all_1001_2000=readRDS(file="T14_4_gblup_prediction_all_1001_2000.rds") +T14_4_gblup_prediction_all_2001_3000=readRDS(file="T14_4_gblup_prediction_all_2001_3000.rds") +T14_4_gblup_prediction_all_3001_4000=readRDS(file="T14_4_gblup_prediction_all_3001_4000.rds") +T14_4_gblup_prediction_all_4001_5000=readRDS(file="T14_4_gblup_prediction_all_4001_5000.rds") +T14_4_gblup_prediction_all_5001_6000=readRDS(file="T14_4_gblup_prediction_all_5001_6000.rds") +T14_4_gblup_prediction_all_6001_7000=readRDS(file="T14_4_gblup_prediction_all_6001_7000.rds") +T14_4_gblup_prediction_all_7001_8000=readRDS(file="T14_4_gblup_prediction_all_7001_8000.rds") +T14_4_gblup_prediction_all_8001_9000=readRDS(file="T14_4_gblup_prediction_all_8001_9000.rds") +T14_4_gblup_prediction_all_9001_10000=readRDS(file="T14_4_gblup_prediction_all_9001_10000.rds") +T14_4_gblup_prediction_all_10001_11000=readRDS(file="T14_4_gblup_prediction_all_10001_11000.rds") +T14_4_gblup_prediction_all_11001_12419=readRDS(file="T14_4_gblup_prediction_all_11001_12419.rds") +T14_4_gblup_prediction_all=c(T14_4_gblup_prediction_all_1_1000,T14_4_gblup_prediction_all_1001_2000,T14_4_gblup_prediction_all_2001_3000,T14_4_gblup_prediction_all_3001_4000,T14_4_gblup_prediction_all_4001_5000,T14_4_gblup_prediction_all_5001_6000,T14_4_gblup_prediction_all_6001_7000,T14_4_gblup_prediction_all_7001_8000,T14_4_gblup_prediction_all_8001_9000,T14_4_gblup_prediction_all_9001_10000,T14_4_gblup_prediction_all_10001_11000,T14_4_gblup_prediction_all_11001_12419) + +T14_4_gblup_variances_all_1_1000=readRDS(file="T14_4_gblup_variances_all_1_1000.rds") +T14_4_gblup_variances_all_1001_2000=readRDS(file="T14_4_gblup_variances_all_1001_2000.rds") +T14_4_gblup_variances_all_2001_3000=readRDS(file="T14_4_gblup_variances_all_2001_3000.rds") +T14_4_gblup_variances_all_3001_4000=readRDS(file="T14_4_gblup_variances_all_3001_4000.rds") +T14_4_gblup_variances_all_4001_5000=readRDS(file="T14_4_gblup_variances_all_4001_5000.rds") +T14_4_gblup_variances_all_5001_6000=readRDS(file="T14_4_gblup_variances_all_5001_6000.rds") +T14_4_gblup_variances_all_6001_7000=readRDS(file="T14_4_gblup_variances_all_6001_7000.rds") +T14_4_gblup_variances_all_7001_8000=readRDS(file="T14_4_gblup_variances_all_7001_8000.rds") +T14_4_gblup_variances_all_8001_9000=readRDS(file="T14_4_gblup_variances_all_8001_9000.rds") +T14_4_gblup_variances_all_9001_10000=readRDS(file="T14_4_gblup_variances_all_9001_10000.rds") +T14_4_gblup_variances_all_10001_11000=readRDS(file="T14_4_gblup_variances_all_10001_11000.rds") +T14_4_gblup_variances_all_11001_12419=readRDS(file="T14_4_gblup_variances_all_11001_12419.rds") +T14_4_gblup_variances_all=c(T14_4_gblup_variances_all_1_1000,T14_4_gblup_variances_all_1001_2000,T14_4_gblup_variances_all_2001_3000,T14_4_gblup_variances_all_3001_4000,T14_4_gblup_variances_all_4001_5000,T14_4_gblup_variances_all_5001_6000,T14_4_gblup_variances_all_6001_7000,T14_4_gblup_variances_all_7001_8000,T14_4_gblup_variances_all_8001_9000,T14_4_gblup_variances_all_9001_10000,T14_4_gblup_variances_all_10001_11000,T14_4_gblup_variances_all_11001_12419) + +saveRDS(T14_4_gblup_prediction_all,"T14_4_gblup_prediction_all.rds") +saveRDS(T14_4_gblup_variances_all,"T14_4_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_4_gfblup_prediction_all_1_1000=readRDS(file="T14_4_gfblup_prediction_all_1_1000.rds") +T14_4_gfblup_prediction_all_1001_2000=readRDS(file="T14_4_gfblup_prediction_all_1001_2000.rds") +T14_4_gfblup_prediction_all_2001_3000=readRDS(file="T14_4_gfblup_prediction_all_2001_3000.rds") +T14_4_gfblup_prediction_all_3001_4000=readRDS(file="T14_4_gfblup_prediction_all_3001_4000.rds") +T14_4_gfblup_prediction_all_4001_5000=readRDS(file="T14_4_gfblup_prediction_all_4001_5000.rds") +T14_4_gfblup_prediction_all_5001_6000=readRDS(file="T14_4_gfblup_prediction_all_5001_6000.rds") +T14_4_gfblup_prediction_all_6001_7000=readRDS(file="T14_4_gfblup_prediction_all_6001_7000.rds") +T14_4_gfblup_prediction_all_7001_8000=readRDS(file="T14_4_gfblup_prediction_all_7001_8000.rds") +T14_4_gfblup_prediction_all_8001_9000=readRDS(file="T14_4_gfblup_prediction_all_8001_9000.rds") +T14_4_gfblup_prediction_all_9001_10000=readRDS(file="T14_4_gfblup_prediction_all_9001_10000.rds") +T14_4_gfblup_prediction_all_10001_11000=readRDS(file="T14_4_gfblup_prediction_all_10001_11000.rds") +T14_4_gfblup_prediction_all_11001_12419=readRDS(file="T14_4_gfblup_prediction_all_11001_12419.rds") + +T14_4_gfblup_variances_all_1_1000=readRDS(file="T14_4_gfblup_variances_all_1_1000.rds") +T14_4_gfblup_variances_all_1001_2000=readRDS(file="T14_4_gfblup_variances_all_1001_2000.rds") +T14_4_gfblup_variances_all_2001_3000=readRDS(file="T14_4_gfblup_variances_all_2001_3000.rds") +T14_4_gfblup_variances_all_3001_4000=readRDS(file="T14_4_gfblup_variances_all_3001_4000.rds") +T14_4_gfblup_variances_all_4001_5000=readRDS(file="T14_4_gfblup_variances_all_4001_5000.rds") +T14_4_gfblup_variances_all_5001_6000=readRDS(file="T14_4_gfblup_variances_all_5001_6000.rds") +T14_4_gfblup_variances_all_6001_7000=readRDS(file="T14_4_gfblup_variances_all_6001_7000.rds") +T14_4_gfblup_variances_all_7001_8000=readRDS(file="T14_4_gfblup_variances_all_7001_8000.rds") +T14_4_gfblup_variances_all_8001_9000=readRDS(file="T14_4_gfblup_variances_all_8001_9000.rds") +T14_4_gfblup_variances_all_9001_10000=readRDS(file="T14_4_gfblup_variances_all_9001_10000.rds") +T14_4_gfblup_variances_all_10001_11000=readRDS(file="T14_4_gfblup_variances_all_10001_11000.rds") +T14_4_gfblup_variances_all_11001_12419=readRDS(file="T14_4_gfblup_variances_all_11001_12419.rds") + +cycles=length(T14_4_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T14_4_gfblup_variances_all=rep(list(list()),cycles) +T14_4_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_1_1000[[r]]) + T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_1001_2000[[r]]) + T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_2001_3000[[r]]) + T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_3001_4000[[r]]) + T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_4001_5000[[r]]) + T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_5001_6000[[r]]) + T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_6001_7000[[r]]) + T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_7001_8000[[r]]) + T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_8001_9000[[r]]) + T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_9001_10000[[r]]) + T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_10001_11000[[r]]) + T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_11001_12419[[r]]) + + T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_1_1000[[r]]) + T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_1001_2000[[r]]) + T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_2001_3000[[r]]) + T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_3001_4000[[r]]) + T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_4001_5000[[r]]) + T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_5001_6000[[r]]) + T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_6001_7000[[r]]) + T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_7001_8000[[r]]) + T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_8001_9000[[r]]) + T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_9001_10000[[r]]) + T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_10001_11000[[r]]) + T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T14_4_gfblup_prediction_all,"T14_4_gfblup_prediction_all.rds") +saveRDS(T14_4_gfblup_variances_all,"T14_4_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_5_gblup_prediction_all_1_1000=readRDS(file="T14_5_gblup_prediction_all_1_1000.rds") +T14_5_gblup_prediction_all_1001_2000=readRDS(file="T14_5_gblup_prediction_all_1001_2000.rds") +T14_5_gblup_prediction_all_2001_3000=readRDS(file="T14_5_gblup_prediction_all_2001_3000.rds") +T14_5_gblup_prediction_all_3001_4000=readRDS(file="T14_5_gblup_prediction_all_3001_4000.rds") +T14_5_gblup_prediction_all_4001_5000=readRDS(file="T14_5_gblup_prediction_all_4001_5000.rds") +T14_5_gblup_prediction_all_5001_6000=readRDS(file="T14_5_gblup_prediction_all_5001_6000.rds") +T14_5_gblup_prediction_all_6001_7000=readRDS(file="T14_5_gblup_prediction_all_6001_7000.rds") +T14_5_gblup_prediction_all_7001_8000=readRDS(file="T14_5_gblup_prediction_all_7001_8000.rds") +T14_5_gblup_prediction_all_8001_9000=readRDS(file="T14_5_gblup_prediction_all_8001_9000.rds") +T14_5_gblup_prediction_all_9001_10000=readRDS(file="T14_5_gblup_prediction_all_9001_10000.rds") +T14_5_gblup_prediction_all_10001_11000=readRDS(file="T14_5_gblup_prediction_all_10001_11000.rds") +T14_5_gblup_prediction_all_11001_12419=readRDS(file="T14_5_gblup_prediction_all_11001_12419.rds") +T14_5_gblup_prediction_all=c(T14_5_gblup_prediction_all_1_1000,T14_5_gblup_prediction_all_1001_2000,T14_5_gblup_prediction_all_2001_3000,T14_5_gblup_prediction_all_3001_4000,T14_5_gblup_prediction_all_4001_5000,T14_5_gblup_prediction_all_5001_6000,T14_5_gblup_prediction_all_6001_7000,T14_5_gblup_prediction_all_7001_8000,T14_5_gblup_prediction_all_8001_9000,T14_5_gblup_prediction_all_9001_10000,T14_5_gblup_prediction_all_10001_11000,T14_5_gblup_prediction_all_11001_12419) + +T14_5_gblup_variances_all_1_1000=readRDS(file="T14_5_gblup_variances_all_1_1000.rds") +T14_5_gblup_variances_all_1001_2000=readRDS(file="T14_5_gblup_variances_all_1001_2000.rds") +T14_5_gblup_variances_all_2001_3000=readRDS(file="T14_5_gblup_variances_all_2001_3000.rds") +T14_5_gblup_variances_all_3001_4000=readRDS(file="T14_5_gblup_variances_all_3001_4000.rds") +T14_5_gblup_variances_all_4001_5000=readRDS(file="T14_5_gblup_variances_all_4001_5000.rds") +T14_5_gblup_variances_all_5001_6000=readRDS(file="T14_5_gblup_variances_all_5001_6000.rds") +T14_5_gblup_variances_all_6001_7000=readRDS(file="T14_5_gblup_variances_all_6001_7000.rds") +T14_5_gblup_variances_all_7001_8000=readRDS(file="T14_5_gblup_variances_all_7001_8000.rds") +T14_5_gblup_variances_all_8001_9000=readRDS(file="T14_5_gblup_variances_all_8001_9000.rds") +T14_5_gblup_variances_all_9001_10000=readRDS(file="T14_5_gblup_variances_all_9001_10000.rds") +T14_5_gblup_variances_all_10001_11000=readRDS(file="T14_5_gblup_variances_all_10001_11000.rds") +T14_5_gblup_variances_all_11001_12419=readRDS(file="T14_5_gblup_variances_all_11001_12419.rds") +T14_5_gblup_variances_all=c(T14_5_gblup_variances_all_1_1000,T14_5_gblup_variances_all_1001_2000,T14_5_gblup_variances_all_2001_3000,T14_5_gblup_variances_all_3001_4000,T14_5_gblup_variances_all_4001_5000,T14_5_gblup_variances_all_5001_6000,T14_5_gblup_variances_all_6001_7000,T14_5_gblup_variances_all_7001_8000,T14_5_gblup_variances_all_8001_9000,T14_5_gblup_variances_all_9001_10000,T14_5_gblup_variances_all_10001_11000,T14_5_gblup_variances_all_11001_12419) + +saveRDS(T14_5_gblup_prediction_all,"T14_5_gblup_prediction_all.rds") +saveRDS(T14_5_gblup_variances_all,"T14_5_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_5_gfblup_prediction_all_1_1000=readRDS(file="T14_5_gfblup_prediction_all_1_1000.rds") +T14_5_gfblup_prediction_all_1001_2000=readRDS(file="T14_5_gfblup_prediction_all_1001_2000.rds") +T14_5_gfblup_prediction_all_2001_3000=readRDS(file="T14_5_gfblup_prediction_all_2001_3000.rds") +T14_5_gfblup_prediction_all_3001_4000=readRDS(file="T14_5_gfblup_prediction_all_3001_4000.rds") +T14_5_gfblup_prediction_all_4001_5000=readRDS(file="T14_5_gfblup_prediction_all_4001_5000.rds") +T14_5_gfblup_prediction_all_5001_6000=readRDS(file="T14_5_gfblup_prediction_all_5001_6000.rds") +T14_5_gfblup_prediction_all_6001_7000=readRDS(file="T14_5_gfblup_prediction_all_6001_7000.rds") +T14_5_gfblup_prediction_all_7001_8000=readRDS(file="T14_5_gfblup_prediction_all_7001_8000.rds") +T14_5_gfblup_prediction_all_8001_9000=readRDS(file="T14_5_gfblup_prediction_all_8001_9000.rds") +T14_5_gfblup_prediction_all_9001_10000=readRDS(file="T14_5_gfblup_prediction_all_9001_10000.rds") +T14_5_gfblup_prediction_all_10001_11000=readRDS(file="T14_5_gfblup_prediction_all_10001_11000.rds") +T14_5_gfblup_prediction_all_11001_12419=readRDS(file="T14_5_gfblup_prediction_all_11001_12419.rds") + +T14_5_gfblup_variances_all_1_1000=readRDS(file="T14_5_gfblup_variances_all_1_1000.rds") +T14_5_gfblup_variances_all_1001_2000=readRDS(file="T14_5_gfblup_variances_all_1001_2000.rds") +T14_5_gfblup_variances_all_2001_3000=readRDS(file="T14_5_gfblup_variances_all_2001_3000.rds") +T14_5_gfblup_variances_all_3001_4000=readRDS(file="T14_5_gfblup_variances_all_3001_4000.rds") +T14_5_gfblup_variances_all_4001_5000=readRDS(file="T14_5_gfblup_variances_all_4001_5000.rds") +T14_5_gfblup_variances_all_5001_6000=readRDS(file="T14_5_gfblup_variances_all_5001_6000.rds") +T14_5_gfblup_variances_all_6001_7000=readRDS(file="T14_5_gfblup_variances_all_6001_7000.rds") +T14_5_gfblup_variances_all_7001_8000=readRDS(file="T14_5_gfblup_variances_all_7001_8000.rds") +T14_5_gfblup_variances_all_8001_9000=readRDS(file="T14_5_gfblup_variances_all_8001_9000.rds") +T14_5_gfblup_variances_all_9001_10000=readRDS(file="T14_5_gfblup_variances_all_9001_10000.rds") +T14_5_gfblup_variances_all_10001_11000=readRDS(file="T14_5_gfblup_variances_all_10001_11000.rds") +T14_5_gfblup_variances_all_11001_12419=readRDS(file="T14_5_gfblup_variances_all_11001_12419.rds") + +cycles=length(T14_5_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T14_5_gfblup_variances_all=rep(list(list()),cycles) +T14_5_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_1_1000[[r]]) + T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_1001_2000[[r]]) + T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_2001_3000[[r]]) + T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_3001_4000[[r]]) + T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_4001_5000[[r]]) + T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_5001_6000[[r]]) + T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_6001_7000[[r]]) + T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_7001_8000[[r]]) + T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_8001_9000[[r]]) + T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_9001_10000[[r]]) + T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_10001_11000[[r]]) + T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_11001_12419[[r]]) + + T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_1_1000[[r]]) + T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_1001_2000[[r]]) + T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_2001_3000[[r]]) + T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_3001_4000[[r]]) + T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_4001_5000[[r]]) + T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_5001_6000[[r]]) + T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_6001_7000[[r]]) + T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_7001_8000[[r]]) + T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_8001_9000[[r]]) + T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_9001_10000[[r]]) + T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_10001_11000[[r]]) + T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T14_5_gfblup_prediction_all,"T14_5_gfblup_prediction_all.rds") +saveRDS(T14_5_gfblup_variances_all,"T14_5_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_6_gblup_prediction_all_1_1000=readRDS(file="T14_6_gblup_prediction_all_1_1000.rds") +T14_6_gblup_prediction_all_1001_2000=readRDS(file="T14_6_gblup_prediction_all_1001_2000.rds") +T14_6_gblup_prediction_all_2001_3000=readRDS(file="T14_6_gblup_prediction_all_2001_3000.rds") +T14_6_gblup_prediction_all_3001_4000=readRDS(file="T14_6_gblup_prediction_all_3001_4000.rds") +T14_6_gblup_prediction_all_4001_5000=readRDS(file="T14_6_gblup_prediction_all_4001_5000.rds") +T14_6_gblup_prediction_all_5001_6000=readRDS(file="T14_6_gblup_prediction_all_5001_6000.rds") +T14_6_gblup_prediction_all_6001_7000=readRDS(file="T14_6_gblup_prediction_all_6001_7000.rds") +T14_6_gblup_prediction_all_7001_8000=readRDS(file="T14_6_gblup_prediction_all_7001_8000.rds") +T14_6_gblup_prediction_all_8001_9000=readRDS(file="T14_6_gblup_prediction_all_8001_9000.rds") +T14_6_gblup_prediction_all_9001_10000=readRDS(file="T14_6_gblup_prediction_all_9001_10000.rds") +T14_6_gblup_prediction_all_10001_11000=readRDS(file="T14_6_gblup_prediction_all_10001_11000.rds") +T14_6_gblup_prediction_all_11001_12419=readRDS(file="T14_6_gblup_prediction_all_11001_12419.rds") +T14_6_gblup_prediction_all=c(T14_6_gblup_prediction_all_1_1000,T14_6_gblup_prediction_all_1001_2000,T14_6_gblup_prediction_all_2001_3000,T14_6_gblup_prediction_all_3001_4000,T14_6_gblup_prediction_all_4001_5000,T14_6_gblup_prediction_all_5001_6000,T14_6_gblup_prediction_all_6001_7000,T14_6_gblup_prediction_all_7001_8000,T14_6_gblup_prediction_all_8001_9000,T14_6_gblup_prediction_all_9001_10000,T14_6_gblup_prediction_all_10001_11000,T14_6_gblup_prediction_all_11001_12419) + +T14_6_gblup_variances_all_1_1000=readRDS(file="T14_6_gblup_variances_all_1_1000.rds") +T14_6_gblup_variances_all_1001_2000=readRDS(file="T14_6_gblup_variances_all_1001_2000.rds") +T14_6_gblup_variances_all_2001_3000=readRDS(file="T14_6_gblup_variances_all_2001_3000.rds") +T14_6_gblup_variances_all_3001_4000=readRDS(file="T14_6_gblup_variances_all_3001_4000.rds") +T14_6_gblup_variances_all_4001_5000=readRDS(file="T14_6_gblup_variances_all_4001_5000.rds") +T14_6_gblup_variances_all_5001_6000=readRDS(file="T14_6_gblup_variances_all_5001_6000.rds") +T14_6_gblup_variances_all_6001_7000=readRDS(file="T14_6_gblup_variances_all_6001_7000.rds") +T14_6_gblup_variances_all_7001_8000=readRDS(file="T14_6_gblup_variances_all_7001_8000.rds") +T14_6_gblup_variances_all_8001_9000=readRDS(file="T14_6_gblup_variances_all_8001_9000.rds") +T14_6_gblup_variances_all_9001_10000=readRDS(file="T14_6_gblup_variances_all_9001_10000.rds") +T14_6_gblup_variances_all_10001_11000=readRDS(file="T14_6_gblup_variances_all_10001_11000.rds") +T14_6_gblup_variances_all_11001_12419=readRDS(file="T14_6_gblup_variances_all_11001_12419.rds") +T14_6_gblup_variances_all=c(T14_6_gblup_variances_all_1_1000,T14_6_gblup_variances_all_1001_2000,T14_6_gblup_variances_all_2001_3000,T14_6_gblup_variances_all_3001_4000,T14_6_gblup_variances_all_4001_5000,T14_6_gblup_variances_all_5001_6000,T14_6_gblup_variances_all_6001_7000,T14_6_gblup_variances_all_7001_8000,T14_6_gblup_variances_all_8001_9000,T14_6_gblup_variances_all_9001_10000,T14_6_gblup_variances_all_10001_11000,T14_6_gblup_variances_all_11001_12419) + +saveRDS(T14_6_gblup_prediction_all,"T14_6_gblup_prediction_all.rds") +saveRDS(T14_6_gblup_variances_all,"T14_6_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_6_gfblup_prediction_all_1_1000=readRDS(file="T14_6_gfblup_prediction_all_1_1000.rds") +T14_6_gfblup_prediction_all_1001_2000=readRDS(file="T14_6_gfblup_prediction_all_1001_2000.rds") +T14_6_gfblup_prediction_all_2001_3000=readRDS(file="T14_6_gfblup_prediction_all_2001_3000.rds") +T14_6_gfblup_prediction_all_3001_4000=readRDS(file="T14_6_gfblup_prediction_all_3001_4000.rds") +T14_6_gfblup_prediction_all_4001_5000=readRDS(file="T14_6_gfblup_prediction_all_4001_5000.rds") +T14_6_gfblup_prediction_all_5001_6000=readRDS(file="T14_6_gfblup_prediction_all_5001_6000.rds") +T14_6_gfblup_prediction_all_6001_7000=readRDS(file="T14_6_gfblup_prediction_all_6001_7000.rds") +T14_6_gfblup_prediction_all_7001_8000=readRDS(file="T14_6_gfblup_prediction_all_7001_8000.rds") +T14_6_gfblup_prediction_all_8001_9000=readRDS(file="T14_6_gfblup_prediction_all_8001_9000.rds") +T14_6_gfblup_prediction_all_9001_10000=readRDS(file="T14_6_gfblup_prediction_all_9001_10000.rds") +T14_6_gfblup_prediction_all_10001_11000=readRDS(file="T14_6_gfblup_prediction_all_10001_11000.rds") +T14_6_gfblup_prediction_all_11001_12419=readRDS(file="T14_6_gfblup_prediction_all_11001_12419.rds") + +T14_6_gfblup_variances_all_1_1000=readRDS(file="T14_6_gfblup_variances_all_1_1000.rds") +T14_6_gfblup_variances_all_1001_2000=readRDS(file="T14_6_gfblup_variances_all_1001_2000.rds") +T14_6_gfblup_variances_all_2001_3000=readRDS(file="T14_6_gfblup_variances_all_2001_3000.rds") +T14_6_gfblup_variances_all_3001_4000=readRDS(file="T14_6_gfblup_variances_all_3001_4000.rds") +T14_6_gfblup_variances_all_4001_5000=readRDS(file="T14_6_gfblup_variances_all_4001_5000.rds") +T14_6_gfblup_variances_all_5001_6000=readRDS(file="T14_6_gfblup_variances_all_5001_6000.rds") +T14_6_gfblup_variances_all_6001_7000=readRDS(file="T14_6_gfblup_variances_all_6001_7000.rds") +T14_6_gfblup_variances_all_7001_8000=readRDS(file="T14_6_gfblup_variances_all_7001_8000.rds") +T14_6_gfblup_variances_all_8001_9000=readRDS(file="T14_6_gfblup_variances_all_8001_9000.rds") +T14_6_gfblup_variances_all_9001_10000=readRDS(file="T14_6_gfblup_variances_all_9001_10000.rds") +T14_6_gfblup_variances_all_10001_11000=readRDS(file="T14_6_gfblup_variances_all_10001_11000.rds") +T14_6_gfblup_variances_all_11001_12419=readRDS(file="T14_6_gfblup_variances_all_11001_12419.rds") + +cycles=length(T14_6_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T14_6_gfblup_variances_all=rep(list(list()),cycles) +T14_6_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_1_1000[[r]]) + T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_1001_2000[[r]]) + T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_2001_3000[[r]]) + T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_3001_4000[[r]]) + T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_4001_5000[[r]]) + T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_5001_6000[[r]]) + T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_6001_7000[[r]]) + T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_7001_8000[[r]]) + T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_8001_9000[[r]]) + T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_9001_10000[[r]]) + T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_10001_11000[[r]]) + T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_11001_12419[[r]]) + + T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_1_1000[[r]]) + T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_1001_2000[[r]]) + T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_2001_3000[[r]]) + T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_3001_4000[[r]]) + T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_4001_5000[[r]]) + T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_5001_6000[[r]]) + T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_6001_7000[[r]]) + T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_7001_8000[[r]]) + T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_8001_9000[[r]]) + T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_9001_10000[[r]]) + T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_10001_11000[[r]]) + T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T14_6_gfblup_prediction_all,"T14_6_gfblup_prediction_all.rds") +saveRDS(T14_6_gfblup_variances_all,"T14_6_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_7_gblup_prediction_all_1_1000=readRDS(file="T14_7_gblup_prediction_all_1_1000.rds") +T14_7_gblup_prediction_all_1001_2000=readRDS(file="T14_7_gblup_prediction_all_1001_2000.rds") +T14_7_gblup_prediction_all_2001_3000=readRDS(file="T14_7_gblup_prediction_all_2001_3000.rds") +T14_7_gblup_prediction_all_3001_4000=readRDS(file="T14_7_gblup_prediction_all_3001_4000.rds") +T14_7_gblup_prediction_all_4001_5000=readRDS(file="T14_7_gblup_prediction_all_4001_5000.rds") +T14_7_gblup_prediction_all_5001_6000=readRDS(file="T14_7_gblup_prediction_all_5001_6000.rds") +T14_7_gblup_prediction_all_6001_7000=readRDS(file="T14_7_gblup_prediction_all_6001_7000.rds") +T14_7_gblup_prediction_all_7001_8000=readRDS(file="T14_7_gblup_prediction_all_7001_8000.rds") +T14_7_gblup_prediction_all_8001_9000=readRDS(file="T14_7_gblup_prediction_all_8001_9000.rds") +T14_7_gblup_prediction_all_9001_10000=readRDS(file="T14_7_gblup_prediction_all_9001_10000.rds") +T14_7_gblup_prediction_all_10001_11000=readRDS(file="T14_7_gblup_prediction_all_10001_11000.rds") +T14_7_gblup_prediction_all_11001_12419=readRDS(file="T14_7_gblup_prediction_all_11001_12419.rds") +T14_7_gblup_prediction_all=c(T14_7_gblup_prediction_all_1_1000,T14_7_gblup_prediction_all_1001_2000,T14_7_gblup_prediction_all_2001_3000,T14_7_gblup_prediction_all_3001_4000,T14_7_gblup_prediction_all_4001_5000,T14_7_gblup_prediction_all_5001_6000,T14_7_gblup_prediction_all_6001_7000,T14_7_gblup_prediction_all_7001_8000,T14_7_gblup_prediction_all_8001_9000,T14_7_gblup_prediction_all_9001_10000,T14_7_gblup_prediction_all_10001_11000,T14_7_gblup_prediction_all_11001_12419) + +T14_7_gblup_variances_all_1_1000=readRDS(file="T14_7_gblup_variances_all_1_1000.rds") +T14_7_gblup_variances_all_1001_2000=readRDS(file="T14_7_gblup_variances_all_1001_2000.rds") +T14_7_gblup_variances_all_2001_3000=readRDS(file="T14_7_gblup_variances_all_2001_3000.rds") +T14_7_gblup_variances_all_3001_4000=readRDS(file="T14_7_gblup_variances_all_3001_4000.rds") +T14_7_gblup_variances_all_4001_5000=readRDS(file="T14_7_gblup_variances_all_4001_5000.rds") +T14_7_gblup_variances_all_5001_6000=readRDS(file="T14_7_gblup_variances_all_5001_6000.rds") +T14_7_gblup_variances_all_6001_7000=readRDS(file="T14_7_gblup_variances_all_6001_7000.rds") +T14_7_gblup_variances_all_7001_8000=readRDS(file="T14_7_gblup_variances_all_7001_8000.rds") +T14_7_gblup_variances_all_8001_9000=readRDS(file="T14_7_gblup_variances_all_8001_9000.rds") +T14_7_gblup_variances_all_9001_10000=readRDS(file="T14_7_gblup_variances_all_9001_10000.rds") +T14_7_gblup_variances_all_10001_11000=readRDS(file="T14_7_gblup_variances_all_10001_11000.rds") +T14_7_gblup_variances_all_11001_12419=readRDS(file="T14_7_gblup_variances_all_11001_12419.rds") +T14_7_gblup_variances_all=c(T14_7_gblup_variances_all_1_1000,T14_7_gblup_variances_all_1001_2000,T14_7_gblup_variances_all_2001_3000,T14_7_gblup_variances_all_3001_4000,T14_7_gblup_variances_all_4001_5000,T14_7_gblup_variances_all_5001_6000,T14_7_gblup_variances_all_6001_7000,T14_7_gblup_variances_all_7001_8000,T14_7_gblup_variances_all_8001_9000,T14_7_gblup_variances_all_9001_10000,T14_7_gblup_variances_all_10001_11000,T14_7_gblup_variances_all_11001_12419) + +saveRDS(T14_7_gblup_prediction_all,"T14_7_gblup_prediction_all.rds") +saveRDS(T14_7_gblup_variances_all,"T14_7_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_7_gfblup_prediction_all_1_1000=readRDS(file="T14_7_gfblup_prediction_all_1_1000.rds") +T14_7_gfblup_prediction_all_1001_2000=readRDS(file="T14_7_gfblup_prediction_all_1001_2000.rds") +T14_7_gfblup_prediction_all_2001_3000=readRDS(file="T14_7_gfblup_prediction_all_2001_3000.rds") +T14_7_gfblup_prediction_all_3001_4000=readRDS(file="T14_7_gfblup_prediction_all_3001_4000.rds") +T14_7_gfblup_prediction_all_4001_5000=readRDS(file="T14_7_gfblup_prediction_all_4001_5000.rds") +T14_7_gfblup_prediction_all_5001_6000=readRDS(file="T14_7_gfblup_prediction_all_5001_6000.rds") +T14_7_gfblup_prediction_all_6001_7000=readRDS(file="T14_7_gfblup_prediction_all_6001_7000.rds") +T14_7_gfblup_prediction_all_7001_8000=readRDS(file="T14_7_gfblup_prediction_all_7001_8000.rds") +T14_7_gfblup_prediction_all_8001_9000=readRDS(file="T14_7_gfblup_prediction_all_8001_9000.rds") +T14_7_gfblup_prediction_all_9001_10000=readRDS(file="T14_7_gfblup_prediction_all_9001_10000.rds") +T14_7_gfblup_prediction_all_10001_11000=readRDS(file="T14_7_gfblup_prediction_all_10001_11000.rds") +T14_7_gfblup_prediction_all_11001_12419=readRDS(file="T14_7_gfblup_prediction_all_11001_12419.rds") + +T14_7_gfblup_variances_all_1_1000=readRDS(file="T14_7_gfblup_variances_all_1_1000.rds") +T14_7_gfblup_variances_all_1001_2000=readRDS(file="T14_7_gfblup_variances_all_1001_2000.rds") +T14_7_gfblup_variances_all_2001_3000=readRDS(file="T14_7_gfblup_variances_all_2001_3000.rds") +T14_7_gfblup_variances_all_3001_4000=readRDS(file="T14_7_gfblup_variances_all_3001_4000.rds") +T14_7_gfblup_variances_all_4001_5000=readRDS(file="T14_7_gfblup_variances_all_4001_5000.rds") +T14_7_gfblup_variances_all_5001_6000=readRDS(file="T14_7_gfblup_variances_all_5001_6000.rds") +T14_7_gfblup_variances_all_6001_7000=readRDS(file="T14_7_gfblup_variances_all_6001_7000.rds") +T14_7_gfblup_variances_all_7001_8000=readRDS(file="T14_7_gfblup_variances_all_7001_8000.rds") +T14_7_gfblup_variances_all_8001_9000=readRDS(file="T14_7_gfblup_variances_all_8001_9000.rds") +T14_7_gfblup_variances_all_9001_10000=readRDS(file="T14_7_gfblup_variances_all_9001_10000.rds") +T14_7_gfblup_variances_all_10001_11000=readRDS(file="T14_7_gfblup_variances_all_10001_11000.rds") +T14_7_gfblup_variances_all_11001_12419=readRDS(file="T14_7_gfblup_variances_all_11001_12419.rds") + +cycles=length(T14_7_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T14_7_gfblup_variances_all=rep(list(list()),cycles) +T14_7_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_1_1000[[r]]) + T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_1001_2000[[r]]) + T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_2001_3000[[r]]) + T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_3001_4000[[r]]) + T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_4001_5000[[r]]) + T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_5001_6000[[r]]) + T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_6001_7000[[r]]) + T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_7001_8000[[r]]) + T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_8001_9000[[r]]) + T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_9001_10000[[r]]) + T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_10001_11000[[r]]) + T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_11001_12419[[r]]) + + T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_1_1000[[r]]) + T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_1001_2000[[r]]) + T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_2001_3000[[r]]) + T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_3001_4000[[r]]) + T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_4001_5000[[r]]) + T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_5001_6000[[r]]) + T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_6001_7000[[r]]) + T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_7001_8000[[r]]) + T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_8001_9000[[r]]) + T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_9001_10000[[r]]) + T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_10001_11000[[r]]) + T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T14_7_gfblup_prediction_all,"T14_7_gfblup_prediction_all.rds") +saveRDS(T14_7_gfblup_variances_all,"T14_7_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_8_gblup_prediction_all_1_1000=readRDS(file="T14_8_gblup_prediction_all_1_1000.rds") +T14_8_gblup_prediction_all_1001_2000=readRDS(file="T14_8_gblup_prediction_all_1001_2000.rds") +T14_8_gblup_prediction_all_2001_3000=readRDS(file="T14_8_gblup_prediction_all_2001_3000.rds") +T14_8_gblup_prediction_all_3001_4000=readRDS(file="T14_8_gblup_prediction_all_3001_4000.rds") +T14_8_gblup_prediction_all_4001_5000=readRDS(file="T14_8_gblup_prediction_all_4001_5000.rds") +T14_8_gblup_prediction_all_5001_6000=readRDS(file="T14_8_gblup_prediction_all_5001_6000.rds") +T14_8_gblup_prediction_all_6001_7000=readRDS(file="T14_8_gblup_prediction_all_6001_7000.rds") +T14_8_gblup_prediction_all_7001_8000=readRDS(file="T14_8_gblup_prediction_all_7001_8000.rds") +T14_8_gblup_prediction_all_8001_9000=readRDS(file="T14_8_gblup_prediction_all_8001_9000.rds") +T14_8_gblup_prediction_all_9001_10000=readRDS(file="T14_8_gblup_prediction_all_9001_10000.rds") +T14_8_gblup_prediction_all_10001_11000=readRDS(file="T14_8_gblup_prediction_all_10001_11000.rds") +T14_8_gblup_prediction_all_11001_12419=readRDS(file="T14_8_gblup_prediction_all_11001_12419.rds") +T14_8_gblup_prediction_all=c(T14_8_gblup_prediction_all_1_1000,T14_8_gblup_prediction_all_1001_2000,T14_8_gblup_prediction_all_2001_3000,T14_8_gblup_prediction_all_3001_4000,T14_8_gblup_prediction_all_4001_5000,T14_8_gblup_prediction_all_5001_6000,T14_8_gblup_prediction_all_6001_7000,T14_8_gblup_prediction_all_7001_8000,T14_8_gblup_prediction_all_8001_9000,T14_8_gblup_prediction_all_9001_10000,T14_8_gblup_prediction_all_10001_11000,T14_8_gblup_prediction_all_11001_12419) + +T14_8_gblup_variances_all_1_1000=readRDS(file="T14_8_gblup_variances_all_1_1000.rds") +T14_8_gblup_variances_all_1001_2000=readRDS(file="T14_8_gblup_variances_all_1001_2000.rds") +T14_8_gblup_variances_all_2001_3000=readRDS(file="T14_8_gblup_variances_all_2001_3000.rds") +T14_8_gblup_variances_all_3001_4000=readRDS(file="T14_8_gblup_variances_all_3001_4000.rds") +T14_8_gblup_variances_all_4001_5000=readRDS(file="T14_8_gblup_variances_all_4001_5000.rds") +T14_8_gblup_variances_all_5001_6000=readRDS(file="T14_8_gblup_variances_all_5001_6000.rds") +T14_8_gblup_variances_all_6001_7000=readRDS(file="T14_8_gblup_variances_all_6001_7000.rds") +T14_8_gblup_variances_all_7001_8000=readRDS(file="T14_8_gblup_variances_all_7001_8000.rds") +T14_8_gblup_variances_all_8001_9000=readRDS(file="T14_8_gblup_variances_all_8001_9000.rds") +T14_8_gblup_variances_all_9001_10000=readRDS(file="T14_8_gblup_variances_all_9001_10000.rds") +T14_8_gblup_variances_all_10001_11000=readRDS(file="T14_8_gblup_variances_all_10001_11000.rds") +T14_8_gblup_variances_all_11001_12419=readRDS(file="T14_8_gblup_variances_all_11001_12419.rds") +T14_8_gblup_variances_all=c(T14_8_gblup_variances_all_1_1000,T14_8_gblup_variances_all_1001_2000,T14_8_gblup_variances_all_2001_3000,T14_8_gblup_variances_all_3001_4000,T14_8_gblup_variances_all_4001_5000,T14_8_gblup_variances_all_5001_6000,T14_8_gblup_variances_all_6001_7000,T14_8_gblup_variances_all_7001_8000,T14_8_gblup_variances_all_8001_9000,T14_8_gblup_variances_all_9001_10000,T14_8_gblup_variances_all_10001_11000,T14_8_gblup_variances_all_11001_12419) + +saveRDS(T14_8_gblup_prediction_all,"T14_8_gblup_prediction_all.rds") +saveRDS(T14_8_gblup_variances_all,"T14_8_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_8_gfblup_prediction_all_1_1000=readRDS(file="T14_8_gfblup_prediction_all_1_1000.rds") +T14_8_gfblup_prediction_all_1001_2000=readRDS(file="T14_8_gfblup_prediction_all_1001_2000.rds") +T14_8_gfblup_prediction_all_2001_3000=readRDS(file="T14_8_gfblup_prediction_all_2001_3000.rds") +T14_8_gfblup_prediction_all_3001_4000=readRDS(file="T14_8_gfblup_prediction_all_3001_4000.rds") +T14_8_gfblup_prediction_all_4001_5000=readRDS(file="T14_8_gfblup_prediction_all_4001_5000.rds") +T14_8_gfblup_prediction_all_5001_6000=readRDS(file="T14_8_gfblup_prediction_all_5001_6000.rds") +T14_8_gfblup_prediction_all_6001_7000=readRDS(file="T14_8_gfblup_prediction_all_6001_7000.rds") +T14_8_gfblup_prediction_all_7001_8000=readRDS(file="T14_8_gfblup_prediction_all_7001_8000.rds") +T14_8_gfblup_prediction_all_8001_9000=readRDS(file="T14_8_gfblup_prediction_all_8001_9000.rds") +T14_8_gfblup_prediction_all_9001_10000=readRDS(file="T14_8_gfblup_prediction_all_9001_10000.rds") +T14_8_gfblup_prediction_all_10001_11000=readRDS(file="T14_8_gfblup_prediction_all_10001_11000.rds") +T14_8_gfblup_prediction_all_11001_12419=readRDS(file="T14_8_gfblup_prediction_all_11001_12419.rds") + +T14_8_gfblup_variances_all_1_1000=readRDS(file="T14_8_gfblup_variances_all_1_1000.rds") +T14_8_gfblup_variances_all_1001_2000=readRDS(file="T14_8_gfblup_variances_all_1001_2000.rds") +T14_8_gfblup_variances_all_2001_3000=readRDS(file="T14_8_gfblup_variances_all_2001_3000.rds") +T14_8_gfblup_variances_all_3001_4000=readRDS(file="T14_8_gfblup_variances_all_3001_4000.rds") +T14_8_gfblup_variances_all_4001_5000=readRDS(file="T14_8_gfblup_variances_all_4001_5000.rds") +T14_8_gfblup_variances_all_5001_6000=readRDS(file="T14_8_gfblup_variances_all_5001_6000.rds") +T14_8_gfblup_variances_all_6001_7000=readRDS(file="T14_8_gfblup_variances_all_6001_7000.rds") +T14_8_gfblup_variances_all_7001_8000=readRDS(file="T14_8_gfblup_variances_all_7001_8000.rds") +T14_8_gfblup_variances_all_8001_9000=readRDS(file="T14_8_gfblup_variances_all_8001_9000.rds") +T14_8_gfblup_variances_all_9001_10000=readRDS(file="T14_8_gfblup_variances_all_9001_10000.rds") +T14_8_gfblup_variances_all_10001_11000=readRDS(file="T14_8_gfblup_variances_all_10001_11000.rds") +T14_8_gfblup_variances_all_11001_12419=readRDS(file="T14_8_gfblup_variances_all_11001_12419.rds") + +cycles=length(T14_8_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T14_8_gfblup_variances_all=rep(list(list()),cycles) +T14_8_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_1_1000[[r]]) + T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_1001_2000[[r]]) + T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_2001_3000[[r]]) + T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_3001_4000[[r]]) + T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_4001_5000[[r]]) + T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_5001_6000[[r]]) + T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_6001_7000[[r]]) + T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_7001_8000[[r]]) + T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_8001_9000[[r]]) + T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_9001_10000[[r]]) + T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_10001_11000[[r]]) + T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_11001_12419[[r]]) + + T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_1_1000[[r]]) + T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_1001_2000[[r]]) + T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_2001_3000[[r]]) + T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_3001_4000[[r]]) + T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_4001_5000[[r]]) + T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_5001_6000[[r]]) + T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_6001_7000[[r]]) + T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_7001_8000[[r]]) + T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_8001_9000[[r]]) + T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_9001_10000[[r]]) + T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_10001_11000[[r]]) + T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T14_8_gfblup_prediction_all,"T14_8_gfblup_prediction_all.rds") +saveRDS(T14_8_gfblup_variances_all,"T14_8_gfblup_variances_all.rds") +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_1_gblup_prediction_all_1_1000=readRDS(file="T15_1_gblup_prediction_all_1_1000.rds") +T15_1_gblup_prediction_all_1001_2000=readRDS(file="T15_1_gblup_prediction_all_1001_2000.rds") +T15_1_gblup_prediction_all_2001_3000=readRDS(file="T15_1_gblup_prediction_all_2001_3000.rds") +T15_1_gblup_prediction_all_3001_4000=readRDS(file="T15_1_gblup_prediction_all_3001_4000.rds") +T15_1_gblup_prediction_all_4001_5000=readRDS(file="T15_1_gblup_prediction_all_4001_5000.rds") +T15_1_gblup_prediction_all_5001_6000=readRDS(file="T15_1_gblup_prediction_all_5001_6000.rds") +T15_1_gblup_prediction_all_6001_7000=readRDS(file="T15_1_gblup_prediction_all_6001_7000.rds") +T15_1_gblup_prediction_all_7001_8000=readRDS(file="T15_1_gblup_prediction_all_7001_8000.rds") +T15_1_gblup_prediction_all_8001_9000=readRDS(file="T15_1_gblup_prediction_all_8001_9000.rds") +T15_1_gblup_prediction_all_9001_10000=readRDS(file="T15_1_gblup_prediction_all_9001_10000.rds") +T15_1_gblup_prediction_all_10001_11000=readRDS(file="T15_1_gblup_prediction_all_10001_11000.rds") +T15_1_gblup_prediction_all_11001_12419=readRDS(file="T15_1_gblup_prediction_all_11001_12419.rds") +T15_1_gblup_prediction_all=c(T15_1_gblup_prediction_all_1_1000,T15_1_gblup_prediction_all_1001_2000,T15_1_gblup_prediction_all_2001_3000,T15_1_gblup_prediction_all_3001_4000,T15_1_gblup_prediction_all_4001_5000,T15_1_gblup_prediction_all_5001_6000,T15_1_gblup_prediction_all_6001_7000,T15_1_gblup_prediction_all_7001_8000,T15_1_gblup_prediction_all_8001_9000,T15_1_gblup_prediction_all_9001_10000,T15_1_gblup_prediction_all_10001_11000,T15_1_gblup_prediction_all_11001_12419) + +T15_1_gblup_variances_all_1_1000=readRDS(file="T15_1_gblup_variances_all_1_1000.rds") +T15_1_gblup_variances_all_1001_2000=readRDS(file="T15_1_gblup_variances_all_1001_2000.rds") +T15_1_gblup_variances_all_2001_3000=readRDS(file="T15_1_gblup_variances_all_2001_3000.rds") +T15_1_gblup_variances_all_3001_4000=readRDS(file="T15_1_gblup_variances_all_3001_4000.rds") +T15_1_gblup_variances_all_4001_5000=readRDS(file="T15_1_gblup_variances_all_4001_5000.rds") +T15_1_gblup_variances_all_5001_6000=readRDS(file="T15_1_gblup_variances_all_5001_6000.rds") +T15_1_gblup_variances_all_6001_7000=readRDS(file="T15_1_gblup_variances_all_6001_7000.rds") +T15_1_gblup_variances_all_7001_8000=readRDS(file="T15_1_gblup_variances_all_7001_8000.rds") +T15_1_gblup_variances_all_8001_9000=readRDS(file="T15_1_gblup_variances_all_8001_9000.rds") +T15_1_gblup_variances_all_9001_10000=readRDS(file="T15_1_gblup_variances_all_9001_10000.rds") +T15_1_gblup_variances_all_10001_11000=readRDS(file="T15_1_gblup_variances_all_10001_11000.rds") +T15_1_gblup_variances_all_11001_12419=readRDS(file="T15_1_gblup_variances_all_11001_12419.rds") +T15_1_gblup_variances_all=c(T15_1_gblup_variances_all_1_1000,T15_1_gblup_variances_all_1001_2000,T15_1_gblup_variances_all_2001_3000,T15_1_gblup_variances_all_3001_4000,T15_1_gblup_variances_all_4001_5000,T15_1_gblup_variances_all_5001_6000,T15_1_gblup_variances_all_6001_7000,T15_1_gblup_variances_all_7001_8000,T15_1_gblup_variances_all_8001_9000,T15_1_gblup_variances_all_9001_10000,T15_1_gblup_variances_all_10001_11000,T15_1_gblup_variances_all_11001_12419) + +saveRDS(T15_1_gblup_prediction_all,"T15_1_gblup_prediction_all.rds") +saveRDS(T15_1_gblup_variances_all,"T15_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_1_gfblup_prediction_all_1_1000=readRDS(file="T15_1_gfblup_prediction_all_1_1000.rds") +T15_1_gfblup_prediction_all_1001_2000=readRDS(file="T15_1_gfblup_prediction_all_1001_2000.rds") +T15_1_gfblup_prediction_all_2001_3000=readRDS(file="T15_1_gfblup_prediction_all_2001_3000.rds") +T15_1_gfblup_prediction_all_3001_4000=readRDS(file="T15_1_gfblup_prediction_all_3001_4000.rds") +T15_1_gfblup_prediction_all_4001_5000=readRDS(file="T15_1_gfblup_prediction_all_4001_5000.rds") +T15_1_gfblup_prediction_all_5001_6000=readRDS(file="T15_1_gfblup_prediction_all_5001_6000.rds") +T15_1_gfblup_prediction_all_6001_7000=readRDS(file="T15_1_gfblup_prediction_all_6001_7000.rds") +T15_1_gfblup_prediction_all_7001_8000=readRDS(file="T15_1_gfblup_prediction_all_7001_8000.rds") +T15_1_gfblup_prediction_all_8001_9000=readRDS(file="T15_1_gfblup_prediction_all_8001_9000.rds") +T15_1_gfblup_prediction_all_9001_10000=readRDS(file="T15_1_gfblup_prediction_all_9001_10000.rds") +T15_1_gfblup_prediction_all_10001_11000=readRDS(file="T15_1_gfblup_prediction_all_10001_11000.rds") +T15_1_gfblup_prediction_all_11001_12419=readRDS(file="T15_1_gfblup_prediction_all_11001_12419.rds") + +T15_1_gfblup_variances_all_1_1000=readRDS(file="T15_1_gfblup_variances_all_1_1000.rds") +T15_1_gfblup_variances_all_1001_2000=readRDS(file="T15_1_gfblup_variances_all_1001_2000.rds") +T15_1_gfblup_variances_all_2001_3000=readRDS(file="T15_1_gfblup_variances_all_2001_3000.rds") +T15_1_gfblup_variances_all_3001_4000=readRDS(file="T15_1_gfblup_variances_all_3001_4000.rds") +T15_1_gfblup_variances_all_4001_5000=readRDS(file="T15_1_gfblup_variances_all_4001_5000.rds") +T15_1_gfblup_variances_all_5001_6000=readRDS(file="T15_1_gfblup_variances_all_5001_6000.rds") +T15_1_gfblup_variances_all_6001_7000=readRDS(file="T15_1_gfblup_variances_all_6001_7000.rds") +T15_1_gfblup_variances_all_7001_8000=readRDS(file="T15_1_gfblup_variances_all_7001_8000.rds") +T15_1_gfblup_variances_all_8001_9000=readRDS(file="T15_1_gfblup_variances_all_8001_9000.rds") +T15_1_gfblup_variances_all_9001_10000=readRDS(file="T15_1_gfblup_variances_all_9001_10000.rds") +T15_1_gfblup_variances_all_10001_11000=readRDS(file="T15_1_gfblup_variances_all_10001_11000.rds") +T15_1_gfblup_variances_all_11001_12419=readRDS(file="T15_1_gfblup_variances_all_11001_12419.rds") + +cycles=length(T15_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T15_1_gfblup_variances_all=rep(list(list()),cycles) +T15_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_1_1000[[r]]) + T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_1001_2000[[r]]) + T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_2001_3000[[r]]) + T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_3001_4000[[r]]) + T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_4001_5000[[r]]) + T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_5001_6000[[r]]) + T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_6001_7000[[r]]) + T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_7001_8000[[r]]) + T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_8001_9000[[r]]) + T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_9001_10000[[r]]) + T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_10001_11000[[r]]) + T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_11001_12419[[r]]) + + T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_1_1000[[r]]) + T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_1001_2000[[r]]) + T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_2001_3000[[r]]) + T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_3001_4000[[r]]) + T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_4001_5000[[r]]) + T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_5001_6000[[r]]) + T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_6001_7000[[r]]) + T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_7001_8000[[r]]) + T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_8001_9000[[r]]) + T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_9001_10000[[r]]) + T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_10001_11000[[r]]) + T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T15_1_gfblup_prediction_all,"T15_1_gfblup_prediction_all.rds") +saveRDS(T15_1_gfblup_variances_all,"T15_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_2_gblup_prediction_all_1_1000=readRDS(file="T15_2_gblup_prediction_all_1_1000.rds") +T15_2_gblup_prediction_all_1001_2000=readRDS(file="T15_2_gblup_prediction_all_1001_2000.rds") +T15_2_gblup_prediction_all_2001_3000=readRDS(file="T15_2_gblup_prediction_all_2001_3000.rds") +T15_2_gblup_prediction_all_3001_4000=readRDS(file="T15_2_gblup_prediction_all_3001_4000.rds") +T15_2_gblup_prediction_all_4001_5000=readRDS(file="T15_2_gblup_prediction_all_4001_5000.rds") +T15_2_gblup_prediction_all_5001_6000=readRDS(file="T15_2_gblup_prediction_all_5001_6000.rds") +T15_2_gblup_prediction_all_6001_7000=readRDS(file="T15_2_gblup_prediction_all_6001_7000.rds") +T15_2_gblup_prediction_all_7001_8000=readRDS(file="T15_2_gblup_prediction_all_7001_8000.rds") +T15_2_gblup_prediction_all_8001_9000=readRDS(file="T15_2_gblup_prediction_all_8001_9000.rds") +T15_2_gblup_prediction_all_9001_10000=readRDS(file="T15_2_gblup_prediction_all_9001_10000.rds") +T15_2_gblup_prediction_all_10001_11000=readRDS(file="T15_2_gblup_prediction_all_10001_11000.rds") +T15_2_gblup_prediction_all_11001_12419=readRDS(file="T15_2_gblup_prediction_all_11001_12419.rds") +T15_2_gblup_prediction_all=c(T15_2_gblup_prediction_all_1_1000,T15_2_gblup_prediction_all_1001_2000,T15_2_gblup_prediction_all_2001_3000,T15_2_gblup_prediction_all_3001_4000,T15_2_gblup_prediction_all_4001_5000,T15_2_gblup_prediction_all_5001_6000,T15_2_gblup_prediction_all_6001_7000,T15_2_gblup_prediction_all_7001_8000,T15_2_gblup_prediction_all_8001_9000,T15_2_gblup_prediction_all_9001_10000,T15_2_gblup_prediction_all_10001_11000,T15_2_gblup_prediction_all_11001_12419) + +T15_2_gblup_variances_all_1_1000=readRDS(file="T15_2_gblup_variances_all_1_1000.rds") +T15_2_gblup_variances_all_1001_2000=readRDS(file="T15_2_gblup_variances_all_1001_2000.rds") +T15_2_gblup_variances_all_2001_3000=readRDS(file="T15_2_gblup_variances_all_2001_3000.rds") +T15_2_gblup_variances_all_3001_4000=readRDS(file="T15_2_gblup_variances_all_3001_4000.rds") +T15_2_gblup_variances_all_4001_5000=readRDS(file="T15_2_gblup_variances_all_4001_5000.rds") +T15_2_gblup_variances_all_5001_6000=readRDS(file="T15_2_gblup_variances_all_5001_6000.rds") +T15_2_gblup_variances_all_6001_7000=readRDS(file="T15_2_gblup_variances_all_6001_7000.rds") +T15_2_gblup_variances_all_7001_8000=readRDS(file="T15_2_gblup_variances_all_7001_8000.rds") +T15_2_gblup_variances_all_8001_9000=readRDS(file="T15_2_gblup_variances_all_8001_9000.rds") +T15_2_gblup_variances_all_9001_10000=readRDS(file="T15_2_gblup_variances_all_9001_10000.rds") +T15_2_gblup_variances_all_10001_11000=readRDS(file="T15_2_gblup_variances_all_10001_11000.rds") +T15_2_gblup_variances_all_11001_12419=readRDS(file="T15_2_gblup_variances_all_11001_12419.rds") +T15_2_gblup_variances_all=c(T15_2_gblup_variances_all_1_1000,T15_2_gblup_variances_all_1001_2000,T15_2_gblup_variances_all_2001_3000,T15_2_gblup_variances_all_3001_4000,T15_2_gblup_variances_all_4001_5000,T15_2_gblup_variances_all_5001_6000,T15_2_gblup_variances_all_6001_7000,T15_2_gblup_variances_all_7001_8000,T15_2_gblup_variances_all_8001_9000,T15_2_gblup_variances_all_9001_10000,T15_2_gblup_variances_all_10001_11000,T15_2_gblup_variances_all_11001_12419) + +saveRDS(T15_2_gblup_prediction_all,"T15_2_gblup_prediction_all.rds") +saveRDS(T15_2_gblup_variances_all,"T15_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_2_gfblup_prediction_all_1_1000=readRDS(file="T15_2_gfblup_prediction_all_1_1000.rds") +T15_2_gfblup_prediction_all_1001_2000=readRDS(file="T15_2_gfblup_prediction_all_1001_2000.rds") +T15_2_gfblup_prediction_all_2001_3000=readRDS(file="T15_2_gfblup_prediction_all_2001_3000.rds") +T15_2_gfblup_prediction_all_3001_4000=readRDS(file="T15_2_gfblup_prediction_all_3001_4000.rds") +T15_2_gfblup_prediction_all_4001_5000=readRDS(file="T15_2_gfblup_prediction_all_4001_5000.rds") +T15_2_gfblup_prediction_all_5001_6000=readRDS(file="T15_2_gfblup_prediction_all_5001_6000.rds") +T15_2_gfblup_prediction_all_6001_7000=readRDS(file="T15_2_gfblup_prediction_all_6001_7000.rds") +T15_2_gfblup_prediction_all_7001_8000=readRDS(file="T15_2_gfblup_prediction_all_7001_8000.rds") +T15_2_gfblup_prediction_all_8001_9000=readRDS(file="T15_2_gfblup_prediction_all_8001_9000.rds") +T15_2_gfblup_prediction_all_9001_10000=readRDS(file="T15_2_gfblup_prediction_all_9001_10000.rds") +T15_2_gfblup_prediction_all_10001_11000=readRDS(file="T15_2_gfblup_prediction_all_10001_11000.rds") +T15_2_gfblup_prediction_all_11001_12419=readRDS(file="T15_2_gfblup_prediction_all_11001_12419.rds") + +T15_2_gfblup_variances_all_1_1000=readRDS(file="T15_2_gfblup_variances_all_1_1000.rds") +T15_2_gfblup_variances_all_1001_2000=readRDS(file="T15_2_gfblup_variances_all_1001_2000.rds") +T15_2_gfblup_variances_all_2001_3000=readRDS(file="T15_2_gfblup_variances_all_2001_3000.rds") +T15_2_gfblup_variances_all_3001_4000=readRDS(file="T15_2_gfblup_variances_all_3001_4000.rds") +T15_2_gfblup_variances_all_4001_5000=readRDS(file="T15_2_gfblup_variances_all_4001_5000.rds") +T15_2_gfblup_variances_all_5001_6000=readRDS(file="T15_2_gfblup_variances_all_5001_6000.rds") +T15_2_gfblup_variances_all_6001_7000=readRDS(file="T15_2_gfblup_variances_all_6001_7000.rds") +T15_2_gfblup_variances_all_7001_8000=readRDS(file="T15_2_gfblup_variances_all_7001_8000.rds") +T15_2_gfblup_variances_all_8001_9000=readRDS(file="T15_2_gfblup_variances_all_8001_9000.rds") +T15_2_gfblup_variances_all_9001_10000=readRDS(file="T15_2_gfblup_variances_all_9001_10000.rds") +T15_2_gfblup_variances_all_10001_11000=readRDS(file="T15_2_gfblup_variances_all_10001_11000.rds") +T15_2_gfblup_variances_all_11001_12419=readRDS(file="T15_2_gfblup_variances_all_11001_12419.rds") + +cycles=length(T15_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T15_2_gfblup_variances_all=rep(list(list()),cycles) +T15_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_1_1000[[r]]) + T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_1001_2000[[r]]) + T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_2001_3000[[r]]) + T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_3001_4000[[r]]) + T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_4001_5000[[r]]) + T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_5001_6000[[r]]) + T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_6001_7000[[r]]) + T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_7001_8000[[r]]) + T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_8001_9000[[r]]) + T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_9001_10000[[r]]) + T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_10001_11000[[r]]) + T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_11001_12419[[r]]) + + T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_1_1000[[r]]) + T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_1001_2000[[r]]) + T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_2001_3000[[r]]) + T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_3001_4000[[r]]) + T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_4001_5000[[r]]) + T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_5001_6000[[r]]) + T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_6001_7000[[r]]) + T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_7001_8000[[r]]) + T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_8001_9000[[r]]) + T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_9001_10000[[r]]) + T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_10001_11000[[r]]) + T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T15_2_gfblup_prediction_all,"T15_2_gfblup_prediction_all.rds") +saveRDS(T15_2_gfblup_variances_all,"T15_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_3_gblup_prediction_all_1_1000=readRDS(file="T15_3_gblup_prediction_all_1_1000.rds") +T15_3_gblup_prediction_all_1001_2000=readRDS(file="T15_3_gblup_prediction_all_1001_2000.rds") +T15_3_gblup_prediction_all_2001_3000=readRDS(file="T15_3_gblup_prediction_all_2001_3000.rds") +T15_3_gblup_prediction_all_3001_4000=readRDS(file="T15_3_gblup_prediction_all_3001_4000.rds") +T15_3_gblup_prediction_all_4001_5000=readRDS(file="T15_3_gblup_prediction_all_4001_5000.rds") +T15_3_gblup_prediction_all_5001_6000=readRDS(file="T15_3_gblup_prediction_all_5001_6000.rds") +T15_3_gblup_prediction_all_6001_7000=readRDS(file="T15_3_gblup_prediction_all_6001_7000.rds") +T15_3_gblup_prediction_all_7001_8000=readRDS(file="T15_3_gblup_prediction_all_7001_8000.rds") +T15_3_gblup_prediction_all_8001_9000=readRDS(file="T15_3_gblup_prediction_all_8001_9000.rds") +T15_3_gblup_prediction_all_9001_10000=readRDS(file="T15_3_gblup_prediction_all_9001_10000.rds") +T15_3_gblup_prediction_all_10001_11000=readRDS(file="T15_3_gblup_prediction_all_10001_11000.rds") +T15_3_gblup_prediction_all_11001_12419=readRDS(file="T15_3_gblup_prediction_all_11001_12419.rds") +T15_3_gblup_prediction_all=c(T15_3_gblup_prediction_all_1_1000,T15_3_gblup_prediction_all_1001_2000,T15_3_gblup_prediction_all_2001_3000,T15_3_gblup_prediction_all_3001_4000,T15_3_gblup_prediction_all_4001_5000,T15_3_gblup_prediction_all_5001_6000,T15_3_gblup_prediction_all_6001_7000,T15_3_gblup_prediction_all_7001_8000,T15_3_gblup_prediction_all_8001_9000,T15_3_gblup_prediction_all_9001_10000,T15_3_gblup_prediction_all_10001_11000,T15_3_gblup_prediction_all_11001_12419) + +T15_3_gblup_variances_all_1_1000=readRDS(file="T15_3_gblup_variances_all_1_1000.rds") +T15_3_gblup_variances_all_1001_2000=readRDS(file="T15_3_gblup_variances_all_1001_2000.rds") +T15_3_gblup_variances_all_2001_3000=readRDS(file="T15_3_gblup_variances_all_2001_3000.rds") +T15_3_gblup_variances_all_3001_4000=readRDS(file="T15_3_gblup_variances_all_3001_4000.rds") +T15_3_gblup_variances_all_4001_5000=readRDS(file="T15_3_gblup_variances_all_4001_5000.rds") +T15_3_gblup_variances_all_5001_6000=readRDS(file="T15_3_gblup_variances_all_5001_6000.rds") +T15_3_gblup_variances_all_6001_7000=readRDS(file="T15_3_gblup_variances_all_6001_7000.rds") +T15_3_gblup_variances_all_7001_8000=readRDS(file="T15_3_gblup_variances_all_7001_8000.rds") +T15_3_gblup_variances_all_8001_9000=readRDS(file="T15_3_gblup_variances_all_8001_9000.rds") +T15_3_gblup_variances_all_9001_10000=readRDS(file="T15_3_gblup_variances_all_9001_10000.rds") +T15_3_gblup_variances_all_10001_11000=readRDS(file="T15_3_gblup_variances_all_10001_11000.rds") +T15_3_gblup_variances_all_11001_12419=readRDS(file="T15_3_gblup_variances_all_11001_12419.rds") +T15_3_gblup_variances_all=c(T15_3_gblup_variances_all_1_1000,T15_3_gblup_variances_all_1001_2000,T15_3_gblup_variances_all_2001_3000,T15_3_gblup_variances_all_3001_4000,T15_3_gblup_variances_all_4001_5000,T15_3_gblup_variances_all_5001_6000,T15_3_gblup_variances_all_6001_7000,T15_3_gblup_variances_all_7001_8000,T15_3_gblup_variances_all_8001_9000,T15_3_gblup_variances_all_9001_10000,T15_3_gblup_variances_all_10001_11000,T15_3_gblup_variances_all_11001_12419) + +saveRDS(T15_3_gblup_prediction_all,"T15_3_gblup_prediction_all.rds") +saveRDS(T15_3_gblup_variances_all,"T15_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_3_gfblup_prediction_all_1_1000=readRDS(file="T15_3_gfblup_prediction_all_1_1000.rds") +T15_3_gfblup_prediction_all_1001_2000=readRDS(file="T15_3_gfblup_prediction_all_1001_2000.rds") +T15_3_gfblup_prediction_all_2001_3000=readRDS(file="T15_3_gfblup_prediction_all_2001_3000.rds") +T15_3_gfblup_prediction_all_3001_4000=readRDS(file="T15_3_gfblup_prediction_all_3001_4000.rds") +T15_3_gfblup_prediction_all_4001_5000=readRDS(file="T15_3_gfblup_prediction_all_4001_5000.rds") +T15_3_gfblup_prediction_all_5001_6000=readRDS(file="T15_3_gfblup_prediction_all_5001_6000.rds") +T15_3_gfblup_prediction_all_6001_7000=readRDS(file="T15_3_gfblup_prediction_all_6001_7000.rds") +T15_3_gfblup_prediction_all_7001_8000=readRDS(file="T15_3_gfblup_prediction_all_7001_8000.rds") +T15_3_gfblup_prediction_all_8001_9000=readRDS(file="T15_3_gfblup_prediction_all_8001_9000.rds") +T15_3_gfblup_prediction_all_9001_10000=readRDS(file="T15_3_gfblup_prediction_all_9001_10000.rds") +T15_3_gfblup_prediction_all_10001_11000=readRDS(file="T15_3_gfblup_prediction_all_10001_11000.rds") +T15_3_gfblup_prediction_all_11001_12419=readRDS(file="T15_3_gfblup_prediction_all_11001_12419.rds") + +T15_3_gfblup_variances_all_1_1000=readRDS(file="T15_3_gfblup_variances_all_1_1000.rds") +T15_3_gfblup_variances_all_1001_2000=readRDS(file="T15_3_gfblup_variances_all_1001_2000.rds") +T15_3_gfblup_variances_all_2001_3000=readRDS(file="T15_3_gfblup_variances_all_2001_3000.rds") +T15_3_gfblup_variances_all_3001_4000=readRDS(file="T15_3_gfblup_variances_all_3001_4000.rds") +T15_3_gfblup_variances_all_4001_5000=readRDS(file="T15_3_gfblup_variances_all_4001_5000.rds") +T15_3_gfblup_variances_all_5001_6000=readRDS(file="T15_3_gfblup_variances_all_5001_6000.rds") +T15_3_gfblup_variances_all_6001_7000=readRDS(file="T15_3_gfblup_variances_all_6001_7000.rds") +T15_3_gfblup_variances_all_7001_8000=readRDS(file="T15_3_gfblup_variances_all_7001_8000.rds") +T15_3_gfblup_variances_all_8001_9000=readRDS(file="T15_3_gfblup_variances_all_8001_9000.rds") +T15_3_gfblup_variances_all_9001_10000=readRDS(file="T15_3_gfblup_variances_all_9001_10000.rds") +T15_3_gfblup_variances_all_10001_11000=readRDS(file="T15_3_gfblup_variances_all_10001_11000.rds") +T15_3_gfblup_variances_all_11001_12419=readRDS(file="T15_3_gfblup_variances_all_11001_12419.rds") + +cycles=length(T15_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T15_3_gfblup_variances_all=rep(list(list()),cycles) +T15_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_1_1000[[r]]) + T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_1001_2000[[r]]) + T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_2001_3000[[r]]) + T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_3001_4000[[r]]) + T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_4001_5000[[r]]) + T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_5001_6000[[r]]) + T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_6001_7000[[r]]) + T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_7001_8000[[r]]) + T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_8001_9000[[r]]) + T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_9001_10000[[r]]) + T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_10001_11000[[r]]) + T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_11001_12419[[r]]) + + T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_1_1000[[r]]) + T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_1001_2000[[r]]) + T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_2001_3000[[r]]) + T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_3001_4000[[r]]) + T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_4001_5000[[r]]) + T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_5001_6000[[r]]) + T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_6001_7000[[r]]) + T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_7001_8000[[r]]) + T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_8001_9000[[r]]) + T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_9001_10000[[r]]) + T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_10001_11000[[r]]) + T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T15_3_gfblup_prediction_all,"T15_3_gfblup_prediction_all.rds") +saveRDS(T15_3_gfblup_variances_all,"T15_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_4_gblup_prediction_all_1_1000=readRDS(file="T15_4_gblup_prediction_all_1_1000.rds") +T15_4_gblup_prediction_all_1001_2000=readRDS(file="T15_4_gblup_prediction_all_1001_2000.rds") +T15_4_gblup_prediction_all_2001_3000=readRDS(file="T15_4_gblup_prediction_all_2001_3000.rds") +T15_4_gblup_prediction_all_3001_4000=readRDS(file="T15_4_gblup_prediction_all_3001_4000.rds") +T15_4_gblup_prediction_all_4001_5000=readRDS(file="T15_4_gblup_prediction_all_4001_5000.rds") +T15_4_gblup_prediction_all_5001_6000=readRDS(file="T15_4_gblup_prediction_all_5001_6000.rds") +T15_4_gblup_prediction_all_6001_7000=readRDS(file="T15_4_gblup_prediction_all_6001_7000.rds") +T15_4_gblup_prediction_all_7001_8000=readRDS(file="T15_4_gblup_prediction_all_7001_8000.rds") +T15_4_gblup_prediction_all_8001_9000=readRDS(file="T15_4_gblup_prediction_all_8001_9000.rds") +T15_4_gblup_prediction_all_9001_10000=readRDS(file="T15_4_gblup_prediction_all_9001_10000.rds") +T15_4_gblup_prediction_all_10001_11000=readRDS(file="T15_4_gblup_prediction_all_10001_11000.rds") +T15_4_gblup_prediction_all_11001_12419=readRDS(file="T15_4_gblup_prediction_all_11001_12419.rds") +T15_4_gblup_prediction_all=c(T15_4_gblup_prediction_all_1_1000,T15_4_gblup_prediction_all_1001_2000,T15_4_gblup_prediction_all_2001_3000,T15_4_gblup_prediction_all_3001_4000,T15_4_gblup_prediction_all_4001_5000,T15_4_gblup_prediction_all_5001_6000,T15_4_gblup_prediction_all_6001_7000,T15_4_gblup_prediction_all_7001_8000,T15_4_gblup_prediction_all_8001_9000,T15_4_gblup_prediction_all_9001_10000,T15_4_gblup_prediction_all_10001_11000,T15_4_gblup_prediction_all_11001_12419) + +T15_4_gblup_variances_all_1_1000=readRDS(file="T15_4_gblup_variances_all_1_1000.rds") +T15_4_gblup_variances_all_1001_2000=readRDS(file="T15_4_gblup_variances_all_1001_2000.rds") +T15_4_gblup_variances_all_2001_3000=readRDS(file="T15_4_gblup_variances_all_2001_3000.rds") +T15_4_gblup_variances_all_3001_4000=readRDS(file="T15_4_gblup_variances_all_3001_4000.rds") +T15_4_gblup_variances_all_4001_5000=readRDS(file="T15_4_gblup_variances_all_4001_5000.rds") +T15_4_gblup_variances_all_5001_6000=readRDS(file="T15_4_gblup_variances_all_5001_6000.rds") +T15_4_gblup_variances_all_6001_7000=readRDS(file="T15_4_gblup_variances_all_6001_7000.rds") +T15_4_gblup_variances_all_7001_8000=readRDS(file="T15_4_gblup_variances_all_7001_8000.rds") +T15_4_gblup_variances_all_8001_9000=readRDS(file="T15_4_gblup_variances_all_8001_9000.rds") +T15_4_gblup_variances_all_9001_10000=readRDS(file="T15_4_gblup_variances_all_9001_10000.rds") +T15_4_gblup_variances_all_10001_11000=readRDS(file="T15_4_gblup_variances_all_10001_11000.rds") +T15_4_gblup_variances_all_11001_12419=readRDS(file="T15_4_gblup_variances_all_11001_12419.rds") +T15_4_gblup_variances_all=c(T15_4_gblup_variances_all_1_1000,T15_4_gblup_variances_all_1001_2000,T15_4_gblup_variances_all_2001_3000,T15_4_gblup_variances_all_3001_4000,T15_4_gblup_variances_all_4001_5000,T15_4_gblup_variances_all_5001_6000,T15_4_gblup_variances_all_6001_7000,T15_4_gblup_variances_all_7001_8000,T15_4_gblup_variances_all_8001_9000,T15_4_gblup_variances_all_9001_10000,T15_4_gblup_variances_all_10001_11000,T15_4_gblup_variances_all_11001_12419) + +saveRDS(T15_4_gblup_prediction_all,"T15_4_gblup_prediction_all.rds") +saveRDS(T15_4_gblup_variances_all,"T15_4_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_4_gfblup_prediction_all_1_1000=readRDS(file="T15_4_gfblup_prediction_all_1_1000.rds") +T15_4_gfblup_prediction_all_1001_2000=readRDS(file="T15_4_gfblup_prediction_all_1001_2000.rds") +T15_4_gfblup_prediction_all_2001_3000=readRDS(file="T15_4_gfblup_prediction_all_2001_3000.rds") +T15_4_gfblup_prediction_all_3001_4000=readRDS(file="T15_4_gfblup_prediction_all_3001_4000.rds") +T15_4_gfblup_prediction_all_4001_5000=readRDS(file="T15_4_gfblup_prediction_all_4001_5000.rds") +T15_4_gfblup_prediction_all_5001_6000=readRDS(file="T15_4_gfblup_prediction_all_5001_6000.rds") +T15_4_gfblup_prediction_all_6001_7000=readRDS(file="T15_4_gfblup_prediction_all_6001_7000.rds") +T15_4_gfblup_prediction_all_7001_8000=readRDS(file="T15_4_gfblup_prediction_all_7001_8000.rds") +T15_4_gfblup_prediction_all_8001_9000=readRDS(file="T15_4_gfblup_prediction_all_8001_9000.rds") +T15_4_gfblup_prediction_all_9001_10000=readRDS(file="T15_4_gfblup_prediction_all_9001_10000.rds") +T15_4_gfblup_prediction_all_10001_11000=readRDS(file="T15_4_gfblup_prediction_all_10001_11000.rds") +T15_4_gfblup_prediction_all_11001_12419=readRDS(file="T15_4_gfblup_prediction_all_11001_12419.rds") + +T15_4_gfblup_variances_all_1_1000=readRDS(file="T15_4_gfblup_variances_all_1_1000.rds") +T15_4_gfblup_variances_all_1001_2000=readRDS(file="T15_4_gfblup_variances_all_1001_2000.rds") +T15_4_gfblup_variances_all_2001_3000=readRDS(file="T15_4_gfblup_variances_all_2001_3000.rds") +T15_4_gfblup_variances_all_3001_4000=readRDS(file="T15_4_gfblup_variances_all_3001_4000.rds") +T15_4_gfblup_variances_all_4001_5000=readRDS(file="T15_4_gfblup_variances_all_4001_5000.rds") +T15_4_gfblup_variances_all_5001_6000=readRDS(file="T15_4_gfblup_variances_all_5001_6000.rds") +T15_4_gfblup_variances_all_6001_7000=readRDS(file="T15_4_gfblup_variances_all_6001_7000.rds") +T15_4_gfblup_variances_all_7001_8000=readRDS(file="T15_4_gfblup_variances_all_7001_8000.rds") +T15_4_gfblup_variances_all_8001_9000=readRDS(file="T15_4_gfblup_variances_all_8001_9000.rds") +T15_4_gfblup_variances_all_9001_10000=readRDS(file="T15_4_gfblup_variances_all_9001_10000.rds") +T15_4_gfblup_variances_all_10001_11000=readRDS(file="T15_4_gfblup_variances_all_10001_11000.rds") +T15_4_gfblup_variances_all_11001_12419=readRDS(file="T15_4_gfblup_variances_all_11001_12419.rds") + +cycles=length(T15_4_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T15_4_gfblup_variances_all=rep(list(list()),cycles) +T15_4_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_1_1000[[r]]) + T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_1001_2000[[r]]) + T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_2001_3000[[r]]) + T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_3001_4000[[r]]) + T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_4001_5000[[r]]) + T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_5001_6000[[r]]) + T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_6001_7000[[r]]) + T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_7001_8000[[r]]) + T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_8001_9000[[r]]) + T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_9001_10000[[r]]) + T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_10001_11000[[r]]) + T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_11001_12419[[r]]) + + T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_1_1000[[r]]) + T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_1001_2000[[r]]) + T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_2001_3000[[r]]) + T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_3001_4000[[r]]) + T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_4001_5000[[r]]) + T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_5001_6000[[r]]) + T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_6001_7000[[r]]) + T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_7001_8000[[r]]) + T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_8001_9000[[r]]) + T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_9001_10000[[r]]) + T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_10001_11000[[r]]) + T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T15_4_gfblup_prediction_all,"T15_4_gfblup_prediction_all.rds") +saveRDS(T15_4_gfblup_variances_all,"T15_4_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_5_gblup_prediction_all_1_1000=readRDS(file="T15_5_gblup_prediction_all_1_1000.rds") +T15_5_gblup_prediction_all_1001_2000=readRDS(file="T15_5_gblup_prediction_all_1001_2000.rds") +T15_5_gblup_prediction_all_2001_3000=readRDS(file="T15_5_gblup_prediction_all_2001_3000.rds") +T15_5_gblup_prediction_all_3001_4000=readRDS(file="T15_5_gblup_prediction_all_3001_4000.rds") +T15_5_gblup_prediction_all_4001_5000=readRDS(file="T15_5_gblup_prediction_all_4001_5000.rds") +T15_5_gblup_prediction_all_5001_6000=readRDS(file="T15_5_gblup_prediction_all_5001_6000.rds") +T15_5_gblup_prediction_all_6001_7000=readRDS(file="T15_5_gblup_prediction_all_6001_7000.rds") +T15_5_gblup_prediction_all_7001_8000=readRDS(file="T15_5_gblup_prediction_all_7001_8000.rds") +T15_5_gblup_prediction_all_8001_9000=readRDS(file="T15_5_gblup_prediction_all_8001_9000.rds") +T15_5_gblup_prediction_all_9001_10000=readRDS(file="T15_5_gblup_prediction_all_9001_10000.rds") +T15_5_gblup_prediction_all_10001_11000=readRDS(file="T15_5_gblup_prediction_all_10001_11000.rds") +T15_5_gblup_prediction_all_11001_12419=readRDS(file="T15_5_gblup_prediction_all_11001_12419.rds") +T15_5_gblup_prediction_all=c(T15_5_gblup_prediction_all_1_1000,T15_5_gblup_prediction_all_1001_2000,T15_5_gblup_prediction_all_2001_3000,T15_5_gblup_prediction_all_3001_4000,T15_5_gblup_prediction_all_4001_5000,T15_5_gblup_prediction_all_5001_6000,T15_5_gblup_prediction_all_6001_7000,T15_5_gblup_prediction_all_7001_8000,T15_5_gblup_prediction_all_8001_9000,T15_5_gblup_prediction_all_9001_10000,T15_5_gblup_prediction_all_10001_11000,T15_5_gblup_prediction_all_11001_12419) + +T15_5_gblup_variances_all_1_1000=readRDS(file="T15_5_gblup_variances_all_1_1000.rds") +T15_5_gblup_variances_all_1001_2000=readRDS(file="T15_5_gblup_variances_all_1001_2000.rds") +T15_5_gblup_variances_all_2001_3000=readRDS(file="T15_5_gblup_variances_all_2001_3000.rds") +T15_5_gblup_variances_all_3001_4000=readRDS(file="T15_5_gblup_variances_all_3001_4000.rds") +T15_5_gblup_variances_all_4001_5000=readRDS(file="T15_5_gblup_variances_all_4001_5000.rds") +T15_5_gblup_variances_all_5001_6000=readRDS(file="T15_5_gblup_variances_all_5001_6000.rds") +T15_5_gblup_variances_all_6001_7000=readRDS(file="T15_5_gblup_variances_all_6001_7000.rds") +T15_5_gblup_variances_all_7001_8000=readRDS(file="T15_5_gblup_variances_all_7001_8000.rds") +T15_5_gblup_variances_all_8001_9000=readRDS(file="T15_5_gblup_variances_all_8001_9000.rds") +T15_5_gblup_variances_all_9001_10000=readRDS(file="T15_5_gblup_variances_all_9001_10000.rds") +T15_5_gblup_variances_all_10001_11000=readRDS(file="T15_5_gblup_variances_all_10001_11000.rds") +T15_5_gblup_variances_all_11001_12419=readRDS(file="T15_5_gblup_variances_all_11001_12419.rds") +T15_5_gblup_variances_all=c(T15_5_gblup_variances_all_1_1000,T15_5_gblup_variances_all_1001_2000,T15_5_gblup_variances_all_2001_3000,T15_5_gblup_variances_all_3001_4000,T15_5_gblup_variances_all_4001_5000,T15_5_gblup_variances_all_5001_6000,T15_5_gblup_variances_all_6001_7000,T15_5_gblup_variances_all_7001_8000,T15_5_gblup_variances_all_8001_9000,T15_5_gblup_variances_all_9001_10000,T15_5_gblup_variances_all_10001_11000,T15_5_gblup_variances_all_11001_12419) + +saveRDS(T15_5_gblup_prediction_all,"T15_5_gblup_prediction_all.rds") +saveRDS(T15_5_gblup_variances_all,"T15_5_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_5_gfblup_prediction_all_1_1000=readRDS(file="T15_5_gfblup_prediction_all_1_1000.rds") +T15_5_gfblup_prediction_all_1001_2000=readRDS(file="T15_5_gfblup_prediction_all_1001_2000.rds") +T15_5_gfblup_prediction_all_2001_3000=readRDS(file="T15_5_gfblup_prediction_all_2001_3000.rds") +T15_5_gfblup_prediction_all_3001_4000=readRDS(file="T15_5_gfblup_prediction_all_3001_4000.rds") +T15_5_gfblup_prediction_all_4001_5000=readRDS(file="T15_5_gfblup_prediction_all_4001_5000.rds") +T15_5_gfblup_prediction_all_5001_6000=readRDS(file="T15_5_gfblup_prediction_all_5001_6000.rds") +T15_5_gfblup_prediction_all_6001_7000=readRDS(file="T15_5_gfblup_prediction_all_6001_7000.rds") +T15_5_gfblup_prediction_all_7001_8000=readRDS(file="T15_5_gfblup_prediction_all_7001_8000.rds") +T15_5_gfblup_prediction_all_8001_9000=readRDS(file="T15_5_gfblup_prediction_all_8001_9000.rds") +T15_5_gfblup_prediction_all_9001_10000=readRDS(file="T15_5_gfblup_prediction_all_9001_10000.rds") +T15_5_gfblup_prediction_all_10001_11000=readRDS(file="T15_5_gfblup_prediction_all_10001_11000.rds") +T15_5_gfblup_prediction_all_11001_12419=readRDS(file="T15_5_gfblup_prediction_all_11001_12419.rds") + +T15_5_gfblup_variances_all_1_1000=readRDS(file="T15_5_gfblup_variances_all_1_1000.rds") +T15_5_gfblup_variances_all_1001_2000=readRDS(file="T15_5_gfblup_variances_all_1001_2000.rds") +T15_5_gfblup_variances_all_2001_3000=readRDS(file="T15_5_gfblup_variances_all_2001_3000.rds") +T15_5_gfblup_variances_all_3001_4000=readRDS(file="T15_5_gfblup_variances_all_3001_4000.rds") +T15_5_gfblup_variances_all_4001_5000=readRDS(file="T15_5_gfblup_variances_all_4001_5000.rds") +T15_5_gfblup_variances_all_5001_6000=readRDS(file="T15_5_gfblup_variances_all_5001_6000.rds") +T15_5_gfblup_variances_all_6001_7000=readRDS(file="T15_5_gfblup_variances_all_6001_7000.rds") +T15_5_gfblup_variances_all_7001_8000=readRDS(file="T15_5_gfblup_variances_all_7001_8000.rds") +T15_5_gfblup_variances_all_8001_9000=readRDS(file="T15_5_gfblup_variances_all_8001_9000.rds") +T15_5_gfblup_variances_all_9001_10000=readRDS(file="T15_5_gfblup_variances_all_9001_10000.rds") +T15_5_gfblup_variances_all_10001_11000=readRDS(file="T15_5_gfblup_variances_all_10001_11000.rds") +T15_5_gfblup_variances_all_11001_12419=readRDS(file="T15_5_gfblup_variances_all_11001_12419.rds") + +cycles=length(T15_5_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T15_5_gfblup_variances_all=rep(list(list()),cycles) +T15_5_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_1_1000[[r]]) + T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_1001_2000[[r]]) + T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_2001_3000[[r]]) + T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_3001_4000[[r]]) + T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_4001_5000[[r]]) + T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_5001_6000[[r]]) + T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_6001_7000[[r]]) + T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_7001_8000[[r]]) + T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_8001_9000[[r]]) + T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_9001_10000[[r]]) + T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_10001_11000[[r]]) + T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_11001_12419[[r]]) + + T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_1_1000[[r]]) + T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_1001_2000[[r]]) + T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_2001_3000[[r]]) + T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_3001_4000[[r]]) + T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_4001_5000[[r]]) + T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_5001_6000[[r]]) + T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_6001_7000[[r]]) + T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_7001_8000[[r]]) + T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_8001_9000[[r]]) + T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_9001_10000[[r]]) + T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_10001_11000[[r]]) + T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T15_5_gfblup_prediction_all,"T15_5_gfblup_prediction_all.rds") +saveRDS(T15_5_gfblup_variances_all,"T15_5_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_6_gblup_prediction_all_1_1000=readRDS(file="T15_6_gblup_prediction_all_1_1000.rds") +T15_6_gblup_prediction_all_1001_2000=readRDS(file="T15_6_gblup_prediction_all_1001_2000.rds") +T15_6_gblup_prediction_all_2001_3000=readRDS(file="T15_6_gblup_prediction_all_2001_3000.rds") +T15_6_gblup_prediction_all_3001_4000=readRDS(file="T15_6_gblup_prediction_all_3001_4000.rds") +T15_6_gblup_prediction_all_4001_5000=readRDS(file="T15_6_gblup_prediction_all_4001_5000.rds") +T15_6_gblup_prediction_all_5001_6000=readRDS(file="T15_6_gblup_prediction_all_5001_6000.rds") +T15_6_gblup_prediction_all_6001_7000=readRDS(file="T15_6_gblup_prediction_all_6001_7000.rds") +T15_6_gblup_prediction_all_7001_8000=readRDS(file="T15_6_gblup_prediction_all_7001_8000.rds") +T15_6_gblup_prediction_all_8001_9000=readRDS(file="T15_6_gblup_prediction_all_8001_9000.rds") +T15_6_gblup_prediction_all_9001_10000=readRDS(file="T15_6_gblup_prediction_all_9001_10000.rds") +T15_6_gblup_prediction_all_10001_11000=readRDS(file="T15_6_gblup_prediction_all_10001_11000.rds") +T15_6_gblup_prediction_all_11001_12419=readRDS(file="T15_6_gblup_prediction_all_11001_12419.rds") +T15_6_gblup_prediction_all=c(T15_6_gblup_prediction_all_1_1000,T15_6_gblup_prediction_all_1001_2000,T15_6_gblup_prediction_all_2001_3000,T15_6_gblup_prediction_all_3001_4000,T15_6_gblup_prediction_all_4001_5000,T15_6_gblup_prediction_all_5001_6000,T15_6_gblup_prediction_all_6001_7000,T15_6_gblup_prediction_all_7001_8000,T15_6_gblup_prediction_all_8001_9000,T15_6_gblup_prediction_all_9001_10000,T15_6_gblup_prediction_all_10001_11000,T15_6_gblup_prediction_all_11001_12419) + +T15_6_gblup_variances_all_1_1000=readRDS(file="T15_6_gblup_variances_all_1_1000.rds") +T15_6_gblup_variances_all_1001_2000=readRDS(file="T15_6_gblup_variances_all_1001_2000.rds") +T15_6_gblup_variances_all_2001_3000=readRDS(file="T15_6_gblup_variances_all_2001_3000.rds") +T15_6_gblup_variances_all_3001_4000=readRDS(file="T15_6_gblup_variances_all_3001_4000.rds") +T15_6_gblup_variances_all_4001_5000=readRDS(file="T15_6_gblup_variances_all_4001_5000.rds") +T15_6_gblup_variances_all_5001_6000=readRDS(file="T15_6_gblup_variances_all_5001_6000.rds") +T15_6_gblup_variances_all_6001_7000=readRDS(file="T15_6_gblup_variances_all_6001_7000.rds") +T15_6_gblup_variances_all_7001_8000=readRDS(file="T15_6_gblup_variances_all_7001_8000.rds") +T15_6_gblup_variances_all_8001_9000=readRDS(file="T15_6_gblup_variances_all_8001_9000.rds") +T15_6_gblup_variances_all_9001_10000=readRDS(file="T15_6_gblup_variances_all_9001_10000.rds") +T15_6_gblup_variances_all_10001_11000=readRDS(file="T15_6_gblup_variances_all_10001_11000.rds") +T15_6_gblup_variances_all_11001_12419=readRDS(file="T15_6_gblup_variances_all_11001_12419.rds") +T15_6_gblup_variances_all=c(T15_6_gblup_variances_all_1_1000,T15_6_gblup_variances_all_1001_2000,T15_6_gblup_variances_all_2001_3000,T15_6_gblup_variances_all_3001_4000,T15_6_gblup_variances_all_4001_5000,T15_6_gblup_variances_all_5001_6000,T15_6_gblup_variances_all_6001_7000,T15_6_gblup_variances_all_7001_8000,T15_6_gblup_variances_all_8001_9000,T15_6_gblup_variances_all_9001_10000,T15_6_gblup_variances_all_10001_11000,T15_6_gblup_variances_all_11001_12419) + +saveRDS(T15_6_gblup_prediction_all,"T15_6_gblup_prediction_all.rds") +saveRDS(T15_6_gblup_variances_all,"T15_6_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_6_gfblup_prediction_all_1_1000=readRDS(file="T15_6_gfblup_prediction_all_1_1000.rds") +T15_6_gfblup_prediction_all_1001_2000=readRDS(file="T15_6_gfblup_prediction_all_1001_2000.rds") +T15_6_gfblup_prediction_all_2001_3000=readRDS(file="T15_6_gfblup_prediction_all_2001_3000.rds") +T15_6_gfblup_prediction_all_3001_4000=readRDS(file="T15_6_gfblup_prediction_all_3001_4000.rds") +T15_6_gfblup_prediction_all_4001_5000=readRDS(file="T15_6_gfblup_prediction_all_4001_5000.rds") +T15_6_gfblup_prediction_all_5001_6000=readRDS(file="T15_6_gfblup_prediction_all_5001_6000.rds") +T15_6_gfblup_prediction_all_6001_7000=readRDS(file="T15_6_gfblup_prediction_all_6001_7000.rds") +T15_6_gfblup_prediction_all_7001_8000=readRDS(file="T15_6_gfblup_prediction_all_7001_8000.rds") +T15_6_gfblup_prediction_all_8001_9000=readRDS(file="T15_6_gfblup_prediction_all_8001_9000.rds") +T15_6_gfblup_prediction_all_9001_10000=readRDS(file="T15_6_gfblup_prediction_all_9001_10000.rds") +T15_6_gfblup_prediction_all_10001_11000=readRDS(file="T15_6_gfblup_prediction_all_10001_11000.rds") +T15_6_gfblup_prediction_all_11001_12419=readRDS(file="T15_6_gfblup_prediction_all_11001_12419.rds") + +T15_6_gfblup_variances_all_1_1000=readRDS(file="T15_6_gfblup_variances_all_1_1000.rds") +T15_6_gfblup_variances_all_1001_2000=readRDS(file="T15_6_gfblup_variances_all_1001_2000.rds") +T15_6_gfblup_variances_all_2001_3000=readRDS(file="T15_6_gfblup_variances_all_2001_3000.rds") +T15_6_gfblup_variances_all_3001_4000=readRDS(file="T15_6_gfblup_variances_all_3001_4000.rds") +T15_6_gfblup_variances_all_4001_5000=readRDS(file="T15_6_gfblup_variances_all_4001_5000.rds") +T15_6_gfblup_variances_all_5001_6000=readRDS(file="T15_6_gfblup_variances_all_5001_6000.rds") +T15_6_gfblup_variances_all_6001_7000=readRDS(file="T15_6_gfblup_variances_all_6001_7000.rds") +T15_6_gfblup_variances_all_7001_8000=readRDS(file="T15_6_gfblup_variances_all_7001_8000.rds") +T15_6_gfblup_variances_all_8001_9000=readRDS(file="T15_6_gfblup_variances_all_8001_9000.rds") +T15_6_gfblup_variances_all_9001_10000=readRDS(file="T15_6_gfblup_variances_all_9001_10000.rds") +T15_6_gfblup_variances_all_10001_11000=readRDS(file="T15_6_gfblup_variances_all_10001_11000.rds") +T15_6_gfblup_variances_all_11001_12419=readRDS(file="T15_6_gfblup_variances_all_11001_12419.rds") + +cycles=length(T15_6_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T15_6_gfblup_variances_all=rep(list(list()),cycles) +T15_6_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_1_1000[[r]]) + T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_1001_2000[[r]]) + T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_2001_3000[[r]]) + T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_3001_4000[[r]]) + T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_4001_5000[[r]]) + T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_5001_6000[[r]]) + T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_6001_7000[[r]]) + T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_7001_8000[[r]]) + T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_8001_9000[[r]]) + T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_9001_10000[[r]]) + T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_10001_11000[[r]]) + T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_11001_12419[[r]]) + + T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_1_1000[[r]]) + T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_1001_2000[[r]]) + T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_2001_3000[[r]]) + T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_3001_4000[[r]]) + T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_4001_5000[[r]]) + T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_5001_6000[[r]]) + T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_6001_7000[[r]]) + T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_7001_8000[[r]]) + T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_8001_9000[[r]]) + T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_9001_10000[[r]]) + T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_10001_11000[[r]]) + T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T15_6_gfblup_prediction_all,"T15_6_gfblup_prediction_all.rds") +saveRDS(T15_6_gfblup_variances_all,"T15_6_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_7_gblup_prediction_all_1_1000=readRDS(file="T15_7_gblup_prediction_all_1_1000.rds") +T15_7_gblup_prediction_all_1001_2000=readRDS(file="T15_7_gblup_prediction_all_1001_2000.rds") +T15_7_gblup_prediction_all_2001_3000=readRDS(file="T15_7_gblup_prediction_all_2001_3000.rds") +T15_7_gblup_prediction_all_3001_4000=readRDS(file="T15_7_gblup_prediction_all_3001_4000.rds") +T15_7_gblup_prediction_all_4001_5000=readRDS(file="T15_7_gblup_prediction_all_4001_5000.rds") +T15_7_gblup_prediction_all_5001_6000=readRDS(file="T15_7_gblup_prediction_all_5001_6000.rds") +T15_7_gblup_prediction_all_6001_7000=readRDS(file="T15_7_gblup_prediction_all_6001_7000.rds") +T15_7_gblup_prediction_all_7001_8000=readRDS(file="T15_7_gblup_prediction_all_7001_8000.rds") +T15_7_gblup_prediction_all_8001_9000=readRDS(file="T15_7_gblup_prediction_all_8001_9000.rds") +T15_7_gblup_prediction_all_9001_10000=readRDS(file="T15_7_gblup_prediction_all_9001_10000.rds") +T15_7_gblup_prediction_all_10001_11000=readRDS(file="T15_7_gblup_prediction_all_10001_11000.rds") +T15_7_gblup_prediction_all_11001_12419=readRDS(file="T15_7_gblup_prediction_all_11001_12419.rds") +T15_7_gblup_prediction_all=c(T15_7_gblup_prediction_all_1_1000,T15_7_gblup_prediction_all_1001_2000,T15_7_gblup_prediction_all_2001_3000,T15_7_gblup_prediction_all_3001_4000,T15_7_gblup_prediction_all_4001_5000,T15_7_gblup_prediction_all_5001_6000,T15_7_gblup_prediction_all_6001_7000,T15_7_gblup_prediction_all_7001_8000,T15_7_gblup_prediction_all_8001_9000,T15_7_gblup_prediction_all_9001_10000,T15_7_gblup_prediction_all_10001_11000,T15_7_gblup_prediction_all_11001_12419) + +T15_7_gblup_variances_all_1_1000=readRDS(file="T15_7_gblup_variances_all_1_1000.rds") +T15_7_gblup_variances_all_1001_2000=readRDS(file="T15_7_gblup_variances_all_1001_2000.rds") +T15_7_gblup_variances_all_2001_3000=readRDS(file="T15_7_gblup_variances_all_2001_3000.rds") +T15_7_gblup_variances_all_3001_4000=readRDS(file="T15_7_gblup_variances_all_3001_4000.rds") +T15_7_gblup_variances_all_4001_5000=readRDS(file="T15_7_gblup_variances_all_4001_5000.rds") +T15_7_gblup_variances_all_5001_6000=readRDS(file="T15_7_gblup_variances_all_5001_6000.rds") +T15_7_gblup_variances_all_6001_7000=readRDS(file="T15_7_gblup_variances_all_6001_7000.rds") +T15_7_gblup_variances_all_7001_8000=readRDS(file="T15_7_gblup_variances_all_7001_8000.rds") +T15_7_gblup_variances_all_8001_9000=readRDS(file="T15_7_gblup_variances_all_8001_9000.rds") +T15_7_gblup_variances_all_9001_10000=readRDS(file="T15_7_gblup_variances_all_9001_10000.rds") +T15_7_gblup_variances_all_10001_11000=readRDS(file="T15_7_gblup_variances_all_10001_11000.rds") +T15_7_gblup_variances_all_11001_12419=readRDS(file="T15_7_gblup_variances_all_11001_12419.rds") +T15_7_gblup_variances_all=c(T15_7_gblup_variances_all_1_1000,T15_7_gblup_variances_all_1001_2000,T15_7_gblup_variances_all_2001_3000,T15_7_gblup_variances_all_3001_4000,T15_7_gblup_variances_all_4001_5000,T15_7_gblup_variances_all_5001_6000,T15_7_gblup_variances_all_6001_7000,T15_7_gblup_variances_all_7001_8000,T15_7_gblup_variances_all_8001_9000,T15_7_gblup_variances_all_9001_10000,T15_7_gblup_variances_all_10001_11000,T15_7_gblup_variances_all_11001_12419) + +saveRDS(T15_7_gblup_prediction_all,"T15_7_gblup_prediction_all.rds") +saveRDS(T15_7_gblup_variances_all,"T15_7_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_7_gfblup_prediction_all_1_1000=readRDS(file="T15_7_gfblup_prediction_all_1_1000.rds") +T15_7_gfblup_prediction_all_1001_2000=readRDS(file="T15_7_gfblup_prediction_all_1001_2000.rds") +T15_7_gfblup_prediction_all_2001_3000=readRDS(file="T15_7_gfblup_prediction_all_2001_3000.rds") +T15_7_gfblup_prediction_all_3001_4000=readRDS(file="T15_7_gfblup_prediction_all_3001_4000.rds") +T15_7_gfblup_prediction_all_4001_5000=readRDS(file="T15_7_gfblup_prediction_all_4001_5000.rds") +T15_7_gfblup_prediction_all_5001_6000=readRDS(file="T15_7_gfblup_prediction_all_5001_6000.rds") +T15_7_gfblup_prediction_all_6001_7000=readRDS(file="T15_7_gfblup_prediction_all_6001_7000.rds") +T15_7_gfblup_prediction_all_7001_8000=readRDS(file="T15_7_gfblup_prediction_all_7001_8000.rds") +T15_7_gfblup_prediction_all_8001_9000=readRDS(file="T15_7_gfblup_prediction_all_8001_9000.rds") +T15_7_gfblup_prediction_all_9001_10000=readRDS(file="T15_7_gfblup_prediction_all_9001_10000.rds") +T15_7_gfblup_prediction_all_10001_11000=readRDS(file="T15_7_gfblup_prediction_all_10001_11000.rds") +T15_7_gfblup_prediction_all_11001_12419=readRDS(file="T15_7_gfblup_prediction_all_11001_12419.rds") + +T15_7_gfblup_variances_all_1_1000=readRDS(file="T15_7_gfblup_variances_all_1_1000.rds") +T15_7_gfblup_variances_all_1001_2000=readRDS(file="T15_7_gfblup_variances_all_1001_2000.rds") +T15_7_gfblup_variances_all_2001_3000=readRDS(file="T15_7_gfblup_variances_all_2001_3000.rds") +T15_7_gfblup_variances_all_3001_4000=readRDS(file="T15_7_gfblup_variances_all_3001_4000.rds") +T15_7_gfblup_variances_all_4001_5000=readRDS(file="T15_7_gfblup_variances_all_4001_5000.rds") +T15_7_gfblup_variances_all_5001_6000=readRDS(file="T15_7_gfblup_variances_all_5001_6000.rds") +T15_7_gfblup_variances_all_6001_7000=readRDS(file="T15_7_gfblup_variances_all_6001_7000.rds") +T15_7_gfblup_variances_all_7001_8000=readRDS(file="T15_7_gfblup_variances_all_7001_8000.rds") +T15_7_gfblup_variances_all_8001_9000=readRDS(file="T15_7_gfblup_variances_all_8001_9000.rds") +T15_7_gfblup_variances_all_9001_10000=readRDS(file="T15_7_gfblup_variances_all_9001_10000.rds") +T15_7_gfblup_variances_all_10001_11000=readRDS(file="T15_7_gfblup_variances_all_10001_11000.rds") +T15_7_gfblup_variances_all_11001_12419=readRDS(file="T15_7_gfblup_variances_all_11001_12419.rds") + +cycles=length(T15_7_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T15_7_gfblup_variances_all=rep(list(list()),cycles) +T15_7_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_1_1000[[r]]) + T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_1001_2000[[r]]) + T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_2001_3000[[r]]) + T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_3001_4000[[r]]) + T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_4001_5000[[r]]) + T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_5001_6000[[r]]) + T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_6001_7000[[r]]) + T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_7001_8000[[r]]) + T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_8001_9000[[r]]) + T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_9001_10000[[r]]) + T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_10001_11000[[r]]) + T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_11001_12419[[r]]) + + T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_1_1000[[r]]) + T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_1001_2000[[r]]) + T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_2001_3000[[r]]) + T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_3001_4000[[r]]) + T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_4001_5000[[r]]) + T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_5001_6000[[r]]) + T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_6001_7000[[r]]) + T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_7001_8000[[r]]) + T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_8001_9000[[r]]) + T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_9001_10000[[r]]) + T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_10001_11000[[r]]) + T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T15_7_gfblup_prediction_all,"T15_7_gfblup_prediction_all.rds") +saveRDS(T15_7_gfblup_variances_all,"T15_7_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_8_gblup_prediction_all_1_1000=readRDS(file="T15_8_gblup_prediction_all_1_1000.rds") +T15_8_gblup_prediction_all_1001_2000=readRDS(file="T15_8_gblup_prediction_all_1001_2000.rds") +T15_8_gblup_prediction_all_2001_3000=readRDS(file="T15_8_gblup_prediction_all_2001_3000.rds") +T15_8_gblup_prediction_all_3001_4000=readRDS(file="T15_8_gblup_prediction_all_3001_4000.rds") +T15_8_gblup_prediction_all_4001_5000=readRDS(file="T15_8_gblup_prediction_all_4001_5000.rds") +T15_8_gblup_prediction_all_5001_6000=readRDS(file="T15_8_gblup_prediction_all_5001_6000.rds") +T15_8_gblup_prediction_all_6001_7000=readRDS(file="T15_8_gblup_prediction_all_6001_7000.rds") +T15_8_gblup_prediction_all_7001_8000=readRDS(file="T15_8_gblup_prediction_all_7001_8000.rds") +T15_8_gblup_prediction_all_8001_9000=readRDS(file="T15_8_gblup_prediction_all_8001_9000.rds") +T15_8_gblup_prediction_all_9001_10000=readRDS(file="T15_8_gblup_prediction_all_9001_10000.rds") +T15_8_gblup_prediction_all_10001_11000=readRDS(file="T15_8_gblup_prediction_all_10001_11000.rds") +T15_8_gblup_prediction_all_11001_12419=readRDS(file="T15_8_gblup_prediction_all_11001_12419.rds") +T15_8_gblup_prediction_all=c(T15_8_gblup_prediction_all_1_1000,T15_8_gblup_prediction_all_1001_2000,T15_8_gblup_prediction_all_2001_3000,T15_8_gblup_prediction_all_3001_4000,T15_8_gblup_prediction_all_4001_5000,T15_8_gblup_prediction_all_5001_6000,T15_8_gblup_prediction_all_6001_7000,T15_8_gblup_prediction_all_7001_8000,T15_8_gblup_prediction_all_8001_9000,T15_8_gblup_prediction_all_9001_10000,T15_8_gblup_prediction_all_10001_11000,T15_8_gblup_prediction_all_11001_12419) + +T15_8_gblup_variances_all_1_1000=readRDS(file="T15_8_gblup_variances_all_1_1000.rds") +T15_8_gblup_variances_all_1001_2000=readRDS(file="T15_8_gblup_variances_all_1001_2000.rds") +T15_8_gblup_variances_all_2001_3000=readRDS(file="T15_8_gblup_variances_all_2001_3000.rds") +T15_8_gblup_variances_all_3001_4000=readRDS(file="T15_8_gblup_variances_all_3001_4000.rds") +T15_8_gblup_variances_all_4001_5000=readRDS(file="T15_8_gblup_variances_all_4001_5000.rds") +T15_8_gblup_variances_all_5001_6000=readRDS(file="T15_8_gblup_variances_all_5001_6000.rds") +T15_8_gblup_variances_all_6001_7000=readRDS(file="T15_8_gblup_variances_all_6001_7000.rds") +T15_8_gblup_variances_all_7001_8000=readRDS(file="T15_8_gblup_variances_all_7001_8000.rds") +T15_8_gblup_variances_all_8001_9000=readRDS(file="T15_8_gblup_variances_all_8001_9000.rds") +T15_8_gblup_variances_all_9001_10000=readRDS(file="T15_8_gblup_variances_all_9001_10000.rds") +T15_8_gblup_variances_all_10001_11000=readRDS(file="T15_8_gblup_variances_all_10001_11000.rds") +T15_8_gblup_variances_all_11001_12419=readRDS(file="T15_8_gblup_variances_all_11001_12419.rds") +T15_8_gblup_variances_all=c(T15_8_gblup_variances_all_1_1000,T15_8_gblup_variances_all_1001_2000,T15_8_gblup_variances_all_2001_3000,T15_8_gblup_variances_all_3001_4000,T15_8_gblup_variances_all_4001_5000,T15_8_gblup_variances_all_5001_6000,T15_8_gblup_variances_all_6001_7000,T15_8_gblup_variances_all_7001_8000,T15_8_gblup_variances_all_8001_9000,T15_8_gblup_variances_all_9001_10000,T15_8_gblup_variances_all_10001_11000,T15_8_gblup_variances_all_11001_12419) + +saveRDS(T15_8_gblup_prediction_all,"T15_8_gblup_prediction_all.rds") +saveRDS(T15_8_gblup_variances_all,"T15_8_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_8_gfblup_prediction_all_1_1000=readRDS(file="T15_8_gfblup_prediction_all_1_1000.rds") +T15_8_gfblup_prediction_all_1001_2000=readRDS(file="T15_8_gfblup_prediction_all_1001_2000.rds") +T15_8_gfblup_prediction_all_2001_3000=readRDS(file="T15_8_gfblup_prediction_all_2001_3000.rds") +T15_8_gfblup_prediction_all_3001_4000=readRDS(file="T15_8_gfblup_prediction_all_3001_4000.rds") +T15_8_gfblup_prediction_all_4001_5000=readRDS(file="T15_8_gfblup_prediction_all_4001_5000.rds") +T15_8_gfblup_prediction_all_5001_6000=readRDS(file="T15_8_gfblup_prediction_all_5001_6000.rds") +T15_8_gfblup_prediction_all_6001_7000=readRDS(file="T15_8_gfblup_prediction_all_6001_7000.rds") +T15_8_gfblup_prediction_all_7001_8000=readRDS(file="T15_8_gfblup_prediction_all_7001_8000.rds") +T15_8_gfblup_prediction_all_8001_9000=readRDS(file="T15_8_gfblup_prediction_all_8001_9000.rds") +T15_8_gfblup_prediction_all_9001_10000=readRDS(file="T15_8_gfblup_prediction_all_9001_10000.rds") +T15_8_gfblup_prediction_all_10001_11000=readRDS(file="T15_8_gfblup_prediction_all_10001_11000.rds") +T15_8_gfblup_prediction_all_11001_12419=readRDS(file="T15_8_gfblup_prediction_all_11001_12419.rds") + +T15_8_gfblup_variances_all_1_1000=readRDS(file="T15_8_gfblup_variances_all_1_1000.rds") +T15_8_gfblup_variances_all_1001_2000=readRDS(file="T15_8_gfblup_variances_all_1001_2000.rds") +T15_8_gfblup_variances_all_2001_3000=readRDS(file="T15_8_gfblup_variances_all_2001_3000.rds") +T15_8_gfblup_variances_all_3001_4000=readRDS(file="T15_8_gfblup_variances_all_3001_4000.rds") +T15_8_gfblup_variances_all_4001_5000=readRDS(file="T15_8_gfblup_variances_all_4001_5000.rds") +T15_8_gfblup_variances_all_5001_6000=readRDS(file="T15_8_gfblup_variances_all_5001_6000.rds") +T15_8_gfblup_variances_all_6001_7000=readRDS(file="T15_8_gfblup_variances_all_6001_7000.rds") +T15_8_gfblup_variances_all_7001_8000=readRDS(file="T15_8_gfblup_variances_all_7001_8000.rds") +T15_8_gfblup_variances_all_8001_9000=readRDS(file="T15_8_gfblup_variances_all_8001_9000.rds") +T15_8_gfblup_variances_all_9001_10000=readRDS(file="T15_8_gfblup_variances_all_9001_10000.rds") +T15_8_gfblup_variances_all_10001_11000=readRDS(file="T15_8_gfblup_variances_all_10001_11000.rds") +T15_8_gfblup_variances_all_11001_12419=readRDS(file="T15_8_gfblup_variances_all_11001_12419.rds") + +cycles=length(T15_8_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T15_8_gfblup_variances_all=rep(list(list()),cycles) +T15_8_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_1_1000[[r]]) + T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_1001_2000[[r]]) + T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_2001_3000[[r]]) + T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_3001_4000[[r]]) + T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_4001_5000[[r]]) + T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_5001_6000[[r]]) + T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_6001_7000[[r]]) + T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_7001_8000[[r]]) + T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_8001_9000[[r]]) + T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_9001_10000[[r]]) + T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_10001_11000[[r]]) + T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_11001_12419[[r]]) + + T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_1_1000[[r]]) + T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_1001_2000[[r]]) + T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_2001_3000[[r]]) + T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_3001_4000[[r]]) + T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_4001_5000[[r]]) + T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_5001_6000[[r]]) + T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_6001_7000[[r]]) + T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_7001_8000[[r]]) + T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_8001_9000[[r]]) + T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_9001_10000[[r]]) + T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_10001_11000[[r]]) + T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T15_8_gfblup_prediction_all,"T15_8_gfblup_prediction_all.rds") +saveRDS(T15_8_gfblup_variances_all,"T15_8_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_1_gblup_prediction_all_1_1000=readRDS(file="T16_1_gblup_prediction_all_1_1000.rds") +T16_1_gblup_prediction_all_1001_2000=readRDS(file="T16_1_gblup_prediction_all_1001_2000.rds") +T16_1_gblup_prediction_all_2001_3000=readRDS(file="T16_1_gblup_prediction_all_2001_3000.rds") +T16_1_gblup_prediction_all_3001_4000=readRDS(file="T16_1_gblup_prediction_all_3001_4000.rds") +T16_1_gblup_prediction_all_4001_5000=readRDS(file="T16_1_gblup_prediction_all_4001_5000.rds") +T16_1_gblup_prediction_all_5001_6000=readRDS(file="T16_1_gblup_prediction_all_5001_6000.rds") +T16_1_gblup_prediction_all_6001_7000=readRDS(file="T16_1_gblup_prediction_all_6001_7000.rds") +T16_1_gblup_prediction_all_7001_8000=readRDS(file="T16_1_gblup_prediction_all_7001_8000.rds") +T16_1_gblup_prediction_all_8001_9000=readRDS(file="T16_1_gblup_prediction_all_8001_9000.rds") +T16_1_gblup_prediction_all_9001_10000=readRDS(file="T16_1_gblup_prediction_all_9001_10000.rds") +T16_1_gblup_prediction_all_10001_11000=readRDS(file="T16_1_gblup_prediction_all_10001_11000.rds") +T16_1_gblup_prediction_all_11001_12419=readRDS(file="T16_1_gblup_prediction_all_11001_12419.rds") +T16_1_gblup_prediction_all=c(T16_1_gblup_prediction_all_1_1000,T16_1_gblup_prediction_all_1001_2000,T16_1_gblup_prediction_all_2001_3000,T16_1_gblup_prediction_all_3001_4000,T16_1_gblup_prediction_all_4001_5000,T16_1_gblup_prediction_all_5001_6000,T16_1_gblup_prediction_all_6001_7000,T16_1_gblup_prediction_all_7001_8000,T16_1_gblup_prediction_all_8001_9000,T16_1_gblup_prediction_all_9001_10000,T16_1_gblup_prediction_all_10001_11000,T16_1_gblup_prediction_all_11001_12419) + +T16_1_gblup_variances_all_1_1000=readRDS(file="T16_1_gblup_variances_all_1_1000.rds") +T16_1_gblup_variances_all_1001_2000=readRDS(file="T16_1_gblup_variances_all_1001_2000.rds") +T16_1_gblup_variances_all_2001_3000=readRDS(file="T16_1_gblup_variances_all_2001_3000.rds") +T16_1_gblup_variances_all_3001_4000=readRDS(file="T16_1_gblup_variances_all_3001_4000.rds") +T16_1_gblup_variances_all_4001_5000=readRDS(file="T16_1_gblup_variances_all_4001_5000.rds") +T16_1_gblup_variances_all_5001_6000=readRDS(file="T16_1_gblup_variances_all_5001_6000.rds") +T16_1_gblup_variances_all_6001_7000=readRDS(file="T16_1_gblup_variances_all_6001_7000.rds") +T16_1_gblup_variances_all_7001_8000=readRDS(file="T16_1_gblup_variances_all_7001_8000.rds") +T16_1_gblup_variances_all_8001_9000=readRDS(file="T16_1_gblup_variances_all_8001_9000.rds") +T16_1_gblup_variances_all_9001_10000=readRDS(file="T16_1_gblup_variances_all_9001_10000.rds") +T16_1_gblup_variances_all_10001_11000=readRDS(file="T16_1_gblup_variances_all_10001_11000.rds") +T16_1_gblup_variances_all_11001_12419=readRDS(file="T16_1_gblup_variances_all_11001_12419.rds") +T16_1_gblup_variances_all=c(T16_1_gblup_variances_all_1_1000,T16_1_gblup_variances_all_1001_2000,T16_1_gblup_variances_all_2001_3000,T16_1_gblup_variances_all_3001_4000,T16_1_gblup_variances_all_4001_5000,T16_1_gblup_variances_all_5001_6000,T16_1_gblup_variances_all_6001_7000,T16_1_gblup_variances_all_7001_8000,T16_1_gblup_variances_all_8001_9000,T16_1_gblup_variances_all_9001_10000,T16_1_gblup_variances_all_10001_11000,T16_1_gblup_variances_all_11001_12419) + +saveRDS(T16_1_gblup_prediction_all,"T16_1_gblup_prediction_all.rds") +saveRDS(T16_1_gblup_variances_all,"T16_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_1_gfblup_prediction_all_1_1000=readRDS(file="T16_1_gfblup_prediction_all_1_1000.rds") +T16_1_gfblup_prediction_all_1001_2000=readRDS(file="T16_1_gfblup_prediction_all_1001_2000.rds") +T16_1_gfblup_prediction_all_2001_3000=readRDS(file="T16_1_gfblup_prediction_all_2001_3000.rds") +T16_1_gfblup_prediction_all_3001_4000=readRDS(file="T16_1_gfblup_prediction_all_3001_4000.rds") +T16_1_gfblup_prediction_all_4001_5000=readRDS(file="T16_1_gfblup_prediction_all_4001_5000.rds") +T16_1_gfblup_prediction_all_5001_6000=readRDS(file="T16_1_gfblup_prediction_all_5001_6000.rds") +T16_1_gfblup_prediction_all_6001_7000=readRDS(file="T16_1_gfblup_prediction_all_6001_7000.rds") +T16_1_gfblup_prediction_all_7001_8000=readRDS(file="T16_1_gfblup_prediction_all_7001_8000.rds") +T16_1_gfblup_prediction_all_8001_9000=readRDS(file="T16_1_gfblup_prediction_all_8001_9000.rds") +T16_1_gfblup_prediction_all_9001_10000=readRDS(file="T16_1_gfblup_prediction_all_9001_10000.rds") +T16_1_gfblup_prediction_all_10001_11000=readRDS(file="T16_1_gfblup_prediction_all_10001_11000.rds") +T16_1_gfblup_prediction_all_11001_12419=readRDS(file="T16_1_gfblup_prediction_all_11001_12419.rds") + +T16_1_gfblup_variances_all_1_1000=readRDS(file="T16_1_gfblup_variances_all_1_1000.rds") +T16_1_gfblup_variances_all_1001_2000=readRDS(file="T16_1_gfblup_variances_all_1001_2000.rds") +T16_1_gfblup_variances_all_2001_3000=readRDS(file="T16_1_gfblup_variances_all_2001_3000.rds") +T16_1_gfblup_variances_all_3001_4000=readRDS(file="T16_1_gfblup_variances_all_3001_4000.rds") +T16_1_gfblup_variances_all_4001_5000=readRDS(file="T16_1_gfblup_variances_all_4001_5000.rds") +T16_1_gfblup_variances_all_5001_6000=readRDS(file="T16_1_gfblup_variances_all_5001_6000.rds") +T16_1_gfblup_variances_all_6001_7000=readRDS(file="T16_1_gfblup_variances_all_6001_7000.rds") +T16_1_gfblup_variances_all_7001_8000=readRDS(file="T16_1_gfblup_variances_all_7001_8000.rds") +T16_1_gfblup_variances_all_8001_9000=readRDS(file="T16_1_gfblup_variances_all_8001_9000.rds") +T16_1_gfblup_variances_all_9001_10000=readRDS(file="T16_1_gfblup_variances_all_9001_10000.rds") +T16_1_gfblup_variances_all_10001_11000=readRDS(file="T16_1_gfblup_variances_all_10001_11000.rds") +T16_1_gfblup_variances_all_11001_12419=readRDS(file="T16_1_gfblup_variances_all_11001_12419.rds") + +cycles=length(T16_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T16_1_gfblup_variances_all=rep(list(list()),cycles) +T16_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_1_1000[[r]]) + T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_1001_2000[[r]]) + T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_2001_3000[[r]]) + T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_3001_4000[[r]]) + T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_4001_5000[[r]]) + T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_5001_6000[[r]]) + T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_6001_7000[[r]]) + T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_7001_8000[[r]]) + T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_8001_9000[[r]]) + T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_9001_10000[[r]]) + T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_10001_11000[[r]]) + T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_11001_12419[[r]]) + + T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_1_1000[[r]]) + T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_1001_2000[[r]]) + T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_2001_3000[[r]]) + T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_3001_4000[[r]]) + T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_4001_5000[[r]]) + T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_5001_6000[[r]]) + T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_6001_7000[[r]]) + T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_7001_8000[[r]]) + T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_8001_9000[[r]]) + T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_9001_10000[[r]]) + T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_10001_11000[[r]]) + T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T16_1_gfblup_prediction_all,"T16_1_gfblup_prediction_all.rds") +saveRDS(T16_1_gfblup_variances_all,"T16_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_2_gblup_prediction_all_1_1000=readRDS(file="T16_2_gblup_prediction_all_1_1000.rds") +T16_2_gblup_prediction_all_1001_2000=readRDS(file="T16_2_gblup_prediction_all_1001_2000.rds") +T16_2_gblup_prediction_all_2001_3000=readRDS(file="T16_2_gblup_prediction_all_2001_3000.rds") +T16_2_gblup_prediction_all_3001_4000=readRDS(file="T16_2_gblup_prediction_all_3001_4000.rds") +T16_2_gblup_prediction_all_4001_5000=readRDS(file="T16_2_gblup_prediction_all_4001_5000.rds") +T16_2_gblup_prediction_all_5001_6000=readRDS(file="T16_2_gblup_prediction_all_5001_6000.rds") +T16_2_gblup_prediction_all_6001_7000=readRDS(file="T16_2_gblup_prediction_all_6001_7000.rds") +T16_2_gblup_prediction_all_7001_8000=readRDS(file="T16_2_gblup_prediction_all_7001_8000.rds") +T16_2_gblup_prediction_all_8001_9000=readRDS(file="T16_2_gblup_prediction_all_8001_9000.rds") +T16_2_gblup_prediction_all_9001_10000=readRDS(file="T16_2_gblup_prediction_all_9001_10000.rds") +T16_2_gblup_prediction_all_10001_11000=readRDS(file="T16_2_gblup_prediction_all_10001_11000.rds") +T16_2_gblup_prediction_all_11001_12419=readRDS(file="T16_2_gblup_prediction_all_11001_12419.rds") +T16_2_gblup_prediction_all=c(T16_2_gblup_prediction_all_1_1000,T16_2_gblup_prediction_all_1001_2000,T16_2_gblup_prediction_all_2001_3000,T16_2_gblup_prediction_all_3001_4000,T16_2_gblup_prediction_all_4001_5000,T16_2_gblup_prediction_all_5001_6000,T16_2_gblup_prediction_all_6001_7000,T16_2_gblup_prediction_all_7001_8000,T16_2_gblup_prediction_all_8001_9000,T16_2_gblup_prediction_all_9001_10000,T16_2_gblup_prediction_all_10001_11000,T16_2_gblup_prediction_all_11001_12419) + +T16_2_gblup_variances_all_1_1000=readRDS(file="T16_2_gblup_variances_all_1_1000.rds") +T16_2_gblup_variances_all_1001_2000=readRDS(file="T16_2_gblup_variances_all_1001_2000.rds") +T16_2_gblup_variances_all_2001_3000=readRDS(file="T16_2_gblup_variances_all_2001_3000.rds") +T16_2_gblup_variances_all_3001_4000=readRDS(file="T16_2_gblup_variances_all_3001_4000.rds") +T16_2_gblup_variances_all_4001_5000=readRDS(file="T16_2_gblup_variances_all_4001_5000.rds") +T16_2_gblup_variances_all_5001_6000=readRDS(file="T16_2_gblup_variances_all_5001_6000.rds") +T16_2_gblup_variances_all_6001_7000=readRDS(file="T16_2_gblup_variances_all_6001_7000.rds") +T16_2_gblup_variances_all_7001_8000=readRDS(file="T16_2_gblup_variances_all_7001_8000.rds") +T16_2_gblup_variances_all_8001_9000=readRDS(file="T16_2_gblup_variances_all_8001_9000.rds") +T16_2_gblup_variances_all_9001_10000=readRDS(file="T16_2_gblup_variances_all_9001_10000.rds") +T16_2_gblup_variances_all_10001_11000=readRDS(file="T16_2_gblup_variances_all_10001_11000.rds") +T16_2_gblup_variances_all_11001_12419=readRDS(file="T16_2_gblup_variances_all_11001_12419.rds") +T16_2_gblup_variances_all=c(T16_2_gblup_variances_all_1_1000,T16_2_gblup_variances_all_1001_2000,T16_2_gblup_variances_all_2001_3000,T16_2_gblup_variances_all_3001_4000,T16_2_gblup_variances_all_4001_5000,T16_2_gblup_variances_all_5001_6000,T16_2_gblup_variances_all_6001_7000,T16_2_gblup_variances_all_7001_8000,T16_2_gblup_variances_all_8001_9000,T16_2_gblup_variances_all_9001_10000,T16_2_gblup_variances_all_10001_11000,T16_2_gblup_variances_all_11001_12419) + +saveRDS(T16_2_gblup_prediction_all,"T16_2_gblup_prediction_all.rds") +saveRDS(T16_2_gblup_variances_all,"T16_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_2_gfblup_prediction_all_1_1000=readRDS(file="T16_2_gfblup_prediction_all_1_1000.rds") +T16_2_gfblup_prediction_all_1001_2000=readRDS(file="T16_2_gfblup_prediction_all_1001_2000.rds") +T16_2_gfblup_prediction_all_2001_3000=readRDS(file="T16_2_gfblup_prediction_all_2001_3000.rds") +T16_2_gfblup_prediction_all_3001_4000=readRDS(file="T16_2_gfblup_prediction_all_3001_4000.rds") +T16_2_gfblup_prediction_all_4001_5000=readRDS(file="T16_2_gfblup_prediction_all_4001_5000.rds") +T16_2_gfblup_prediction_all_5001_6000=readRDS(file="T16_2_gfblup_prediction_all_5001_6000.rds") +T16_2_gfblup_prediction_all_6001_7000=readRDS(file="T16_2_gfblup_prediction_all_6001_7000.rds") +T16_2_gfblup_prediction_all_7001_8000=readRDS(file="T16_2_gfblup_prediction_all_7001_8000.rds") +T16_2_gfblup_prediction_all_8001_9000=readRDS(file="T16_2_gfblup_prediction_all_8001_9000.rds") +T16_2_gfblup_prediction_all_9001_10000=readRDS(file="T16_2_gfblup_prediction_all_9001_10000.rds") +T16_2_gfblup_prediction_all_10001_11000=readRDS(file="T16_2_gfblup_prediction_all_10001_11000.rds") +T16_2_gfblup_prediction_all_11001_12419=readRDS(file="T16_2_gfblup_prediction_all_11001_12419.rds") + +T16_2_gfblup_variances_all_1_1000=readRDS(file="T16_2_gfblup_variances_all_1_1000.rds") +T16_2_gfblup_variances_all_1001_2000=readRDS(file="T16_2_gfblup_variances_all_1001_2000.rds") +T16_2_gfblup_variances_all_2001_3000=readRDS(file="T16_2_gfblup_variances_all_2001_3000.rds") +T16_2_gfblup_variances_all_3001_4000=readRDS(file="T16_2_gfblup_variances_all_3001_4000.rds") +T16_2_gfblup_variances_all_4001_5000=readRDS(file="T16_2_gfblup_variances_all_4001_5000.rds") +T16_2_gfblup_variances_all_5001_6000=readRDS(file="T16_2_gfblup_variances_all_5001_6000.rds") +T16_2_gfblup_variances_all_6001_7000=readRDS(file="T16_2_gfblup_variances_all_6001_7000.rds") +T16_2_gfblup_variances_all_7001_8000=readRDS(file="T16_2_gfblup_variances_all_7001_8000.rds") +T16_2_gfblup_variances_all_8001_9000=readRDS(file="T16_2_gfblup_variances_all_8001_9000.rds") +T16_2_gfblup_variances_all_9001_10000=readRDS(file="T16_2_gfblup_variances_all_9001_10000.rds") +T16_2_gfblup_variances_all_10001_11000=readRDS(file="T16_2_gfblup_variances_all_10001_11000.rds") +T16_2_gfblup_variances_all_11001_12419=readRDS(file="T16_2_gfblup_variances_all_11001_12419.rds") + +cycles=length(T16_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T16_2_gfblup_variances_all=rep(list(list()),cycles) +T16_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_1_1000[[r]]) + T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_1001_2000[[r]]) + T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_2001_3000[[r]]) + T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_3001_4000[[r]]) + T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_4001_5000[[r]]) + T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_5001_6000[[r]]) + T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_6001_7000[[r]]) + T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_7001_8000[[r]]) + T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_8001_9000[[r]]) + T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_9001_10000[[r]]) + T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_10001_11000[[r]]) + T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_11001_12419[[r]]) + + T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_1_1000[[r]]) + T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_1001_2000[[r]]) + T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_2001_3000[[r]]) + T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_3001_4000[[r]]) + T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_4001_5000[[r]]) + T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_5001_6000[[r]]) + T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_6001_7000[[r]]) + T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_7001_8000[[r]]) + T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_8001_9000[[r]]) + T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_9001_10000[[r]]) + T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_10001_11000[[r]]) + T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T16_2_gfblup_prediction_all,"T16_2_gfblup_prediction_all.rds") +saveRDS(T16_2_gfblup_variances_all,"T16_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_3_gblup_prediction_all_1_1000=readRDS(file="T16_3_gblup_prediction_all_1_1000.rds") +T16_3_gblup_prediction_all_1001_2000=readRDS(file="T16_3_gblup_prediction_all_1001_2000.rds") +T16_3_gblup_prediction_all_2001_3000=readRDS(file="T16_3_gblup_prediction_all_2001_3000.rds") +T16_3_gblup_prediction_all_3001_4000=readRDS(file="T16_3_gblup_prediction_all_3001_4000.rds") +T16_3_gblup_prediction_all_4001_5000=readRDS(file="T16_3_gblup_prediction_all_4001_5000.rds") +T16_3_gblup_prediction_all_5001_6000=readRDS(file="T16_3_gblup_prediction_all_5001_6000.rds") +T16_3_gblup_prediction_all_6001_7000=readRDS(file="T16_3_gblup_prediction_all_6001_7000.rds") +T16_3_gblup_prediction_all_7001_8000=readRDS(file="T16_3_gblup_prediction_all_7001_8000.rds") +T16_3_gblup_prediction_all_8001_9000=readRDS(file="T16_3_gblup_prediction_all_8001_9000.rds") +T16_3_gblup_prediction_all_9001_10000=readRDS(file="T16_3_gblup_prediction_all_9001_10000.rds") +T16_3_gblup_prediction_all_10001_11000=readRDS(file="T16_3_gblup_prediction_all_10001_11000.rds") +T16_3_gblup_prediction_all_11001_12419=readRDS(file="T16_3_gblup_prediction_all_11001_12419.rds") +T16_3_gblup_prediction_all=c(T16_3_gblup_prediction_all_1_1000,T16_3_gblup_prediction_all_1001_2000,T16_3_gblup_prediction_all_2001_3000,T16_3_gblup_prediction_all_3001_4000,T16_3_gblup_prediction_all_4001_5000,T16_3_gblup_prediction_all_5001_6000,T16_3_gblup_prediction_all_6001_7000,T16_3_gblup_prediction_all_7001_8000,T16_3_gblup_prediction_all_8001_9000,T16_3_gblup_prediction_all_9001_10000,T16_3_gblup_prediction_all_10001_11000,T16_3_gblup_prediction_all_11001_12419) + +T16_3_gblup_variances_all_1_1000=readRDS(file="T16_3_gblup_variances_all_1_1000.rds") +T16_3_gblup_variances_all_1001_2000=readRDS(file="T16_3_gblup_variances_all_1001_2000.rds") +T16_3_gblup_variances_all_2001_3000=readRDS(file="T16_3_gblup_variances_all_2001_3000.rds") +T16_3_gblup_variances_all_3001_4000=readRDS(file="T16_3_gblup_variances_all_3001_4000.rds") +T16_3_gblup_variances_all_4001_5000=readRDS(file="T16_3_gblup_variances_all_4001_5000.rds") +T16_3_gblup_variances_all_5001_6000=readRDS(file="T16_3_gblup_variances_all_5001_6000.rds") +T16_3_gblup_variances_all_6001_7000=readRDS(file="T16_3_gblup_variances_all_6001_7000.rds") +T16_3_gblup_variances_all_7001_8000=readRDS(file="T16_3_gblup_variances_all_7001_8000.rds") +T16_3_gblup_variances_all_8001_9000=readRDS(file="T16_3_gblup_variances_all_8001_9000.rds") +T16_3_gblup_variances_all_9001_10000=readRDS(file="T16_3_gblup_variances_all_9001_10000.rds") +T16_3_gblup_variances_all_10001_11000=readRDS(file="T16_3_gblup_variances_all_10001_11000.rds") +T16_3_gblup_variances_all_11001_12419=readRDS(file="T16_3_gblup_variances_all_11001_12419.rds") +T16_3_gblup_variances_all=c(T16_3_gblup_variances_all_1_1000,T16_3_gblup_variances_all_1001_2000,T16_3_gblup_variances_all_2001_3000,T16_3_gblup_variances_all_3001_4000,T16_3_gblup_variances_all_4001_5000,T16_3_gblup_variances_all_5001_6000,T16_3_gblup_variances_all_6001_7000,T16_3_gblup_variances_all_7001_8000,T16_3_gblup_variances_all_8001_9000,T16_3_gblup_variances_all_9001_10000,T16_3_gblup_variances_all_10001_11000,T16_3_gblup_variances_all_11001_12419) + +saveRDS(T16_3_gblup_prediction_all,"T16_3_gblup_prediction_all.rds") +saveRDS(T16_3_gblup_variances_all,"T16_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_3_gfblup_prediction_all_1_1000=readRDS(file="T16_3_gfblup_prediction_all_1_1000.rds") +T16_3_gfblup_prediction_all_1001_2000=readRDS(file="T16_3_gfblup_prediction_all_1001_2000.rds") +T16_3_gfblup_prediction_all_2001_3000=readRDS(file="T16_3_gfblup_prediction_all_2001_3000.rds") +T16_3_gfblup_prediction_all_3001_4000=readRDS(file="T16_3_gfblup_prediction_all_3001_4000.rds") +T16_3_gfblup_prediction_all_4001_5000=readRDS(file="T16_3_gfblup_prediction_all_4001_5000.rds") +T16_3_gfblup_prediction_all_5001_6000=readRDS(file="T16_3_gfblup_prediction_all_5001_6000.rds") +T16_3_gfblup_prediction_all_6001_7000=readRDS(file="T16_3_gfblup_prediction_all_6001_7000.rds") +T16_3_gfblup_prediction_all_7001_8000=readRDS(file="T16_3_gfblup_prediction_all_7001_8000.rds") +T16_3_gfblup_prediction_all_8001_9000=readRDS(file="T16_3_gfblup_prediction_all_8001_9000.rds") +T16_3_gfblup_prediction_all_9001_10000=readRDS(file="T16_3_gfblup_prediction_all_9001_10000.rds") +T16_3_gfblup_prediction_all_10001_11000=readRDS(file="T16_3_gfblup_prediction_all_10001_11000.rds") +T16_3_gfblup_prediction_all_11001_12419=readRDS(file="T16_3_gfblup_prediction_all_11001_12419.rds") + +T16_3_gfblup_variances_all_1_1000=readRDS(file="T16_3_gfblup_variances_all_1_1000.rds") +T16_3_gfblup_variances_all_1001_2000=readRDS(file="T16_3_gfblup_variances_all_1001_2000.rds") +T16_3_gfblup_variances_all_2001_3000=readRDS(file="T16_3_gfblup_variances_all_2001_3000.rds") +T16_3_gfblup_variances_all_3001_4000=readRDS(file="T16_3_gfblup_variances_all_3001_4000.rds") +T16_3_gfblup_variances_all_4001_5000=readRDS(file="T16_3_gfblup_variances_all_4001_5000.rds") +T16_3_gfblup_variances_all_5001_6000=readRDS(file="T16_3_gfblup_variances_all_5001_6000.rds") +T16_3_gfblup_variances_all_6001_7000=readRDS(file="T16_3_gfblup_variances_all_6001_7000.rds") +T16_3_gfblup_variances_all_7001_8000=readRDS(file="T16_3_gfblup_variances_all_7001_8000.rds") +T16_3_gfblup_variances_all_8001_9000=readRDS(file="T16_3_gfblup_variances_all_8001_9000.rds") +T16_3_gfblup_variances_all_9001_10000=readRDS(file="T16_3_gfblup_variances_all_9001_10000.rds") +T16_3_gfblup_variances_all_10001_11000=readRDS(file="T16_3_gfblup_variances_all_10001_11000.rds") +T16_3_gfblup_variances_all_11001_12419=readRDS(file="T16_3_gfblup_variances_all_11001_12419.rds") + +cycles=length(T16_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T16_3_gfblup_variances_all=rep(list(list()),cycles) +T16_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_1_1000[[r]]) + T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_1001_2000[[r]]) + T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_2001_3000[[r]]) + T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_3001_4000[[r]]) + T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_4001_5000[[r]]) + T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_5001_6000[[r]]) + T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_6001_7000[[r]]) + T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_7001_8000[[r]]) + T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_8001_9000[[r]]) + T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_9001_10000[[r]]) + T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_10001_11000[[r]]) + T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_11001_12419[[r]]) + + T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_1_1000[[r]]) + T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_1001_2000[[r]]) + T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_2001_3000[[r]]) + T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_3001_4000[[r]]) + T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_4001_5000[[r]]) + T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_5001_6000[[r]]) + T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_6001_7000[[r]]) + T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_7001_8000[[r]]) + T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_8001_9000[[r]]) + T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_9001_10000[[r]]) + T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_10001_11000[[r]]) + T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T16_3_gfblup_prediction_all,"T16_3_gfblup_prediction_all.rds") +saveRDS(T16_3_gfblup_variances_all,"T16_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_4_gblup_prediction_all_1_1000=readRDS(file="T16_4_gblup_prediction_all_1_1000.rds") +T16_4_gblup_prediction_all_1001_2000=readRDS(file="T16_4_gblup_prediction_all_1001_2000.rds") +T16_4_gblup_prediction_all_2001_3000=readRDS(file="T16_4_gblup_prediction_all_2001_3000.rds") +T16_4_gblup_prediction_all_3001_4000=readRDS(file="T16_4_gblup_prediction_all_3001_4000.rds") +T16_4_gblup_prediction_all_4001_5000=readRDS(file="T16_4_gblup_prediction_all_4001_5000.rds") +T16_4_gblup_prediction_all_5001_6000=readRDS(file="T16_4_gblup_prediction_all_5001_6000.rds") +T16_4_gblup_prediction_all_6001_7000=readRDS(file="T16_4_gblup_prediction_all_6001_7000.rds") +T16_4_gblup_prediction_all_7001_8000=readRDS(file="T16_4_gblup_prediction_all_7001_8000.rds") +T16_4_gblup_prediction_all_8001_9000=readRDS(file="T16_4_gblup_prediction_all_8001_9000.rds") +T16_4_gblup_prediction_all_9001_10000=readRDS(file="T16_4_gblup_prediction_all_9001_10000.rds") +T16_4_gblup_prediction_all_10001_11000=readRDS(file="T16_4_gblup_prediction_all_10001_11000.rds") +T16_4_gblup_prediction_all_11001_12419=readRDS(file="T16_4_gblup_prediction_all_11001_12419.rds") +T16_4_gblup_prediction_all=c(T16_4_gblup_prediction_all_1_1000,T16_4_gblup_prediction_all_1001_2000,T16_4_gblup_prediction_all_2001_3000,T16_4_gblup_prediction_all_3001_4000,T16_4_gblup_prediction_all_4001_5000,T16_4_gblup_prediction_all_5001_6000,T16_4_gblup_prediction_all_6001_7000,T16_4_gblup_prediction_all_7001_8000,T16_4_gblup_prediction_all_8001_9000,T16_4_gblup_prediction_all_9001_10000,T16_4_gblup_prediction_all_10001_11000,T16_4_gblup_prediction_all_11001_12419) + +T16_4_gblup_variances_all_1_1000=readRDS(file="T16_4_gblup_variances_all_1_1000.rds") +T16_4_gblup_variances_all_1001_2000=readRDS(file="T16_4_gblup_variances_all_1001_2000.rds") +T16_4_gblup_variances_all_2001_3000=readRDS(file="T16_4_gblup_variances_all_2001_3000.rds") +T16_4_gblup_variances_all_3001_4000=readRDS(file="T16_4_gblup_variances_all_3001_4000.rds") +T16_4_gblup_variances_all_4001_5000=readRDS(file="T16_4_gblup_variances_all_4001_5000.rds") +T16_4_gblup_variances_all_5001_6000=readRDS(file="T16_4_gblup_variances_all_5001_6000.rds") +T16_4_gblup_variances_all_6001_7000=readRDS(file="T16_4_gblup_variances_all_6001_7000.rds") +T16_4_gblup_variances_all_7001_8000=readRDS(file="T16_4_gblup_variances_all_7001_8000.rds") +T16_4_gblup_variances_all_8001_9000=readRDS(file="T16_4_gblup_variances_all_8001_9000.rds") +T16_4_gblup_variances_all_9001_10000=readRDS(file="T16_4_gblup_variances_all_9001_10000.rds") +T16_4_gblup_variances_all_10001_11000=readRDS(file="T16_4_gblup_variances_all_10001_11000.rds") +T16_4_gblup_variances_all_11001_12419=readRDS(file="T16_4_gblup_variances_all_11001_12419.rds") +T16_4_gblup_variances_all=c(T16_4_gblup_variances_all_1_1000,T16_4_gblup_variances_all_1001_2000,T16_4_gblup_variances_all_2001_3000,T16_4_gblup_variances_all_3001_4000,T16_4_gblup_variances_all_4001_5000,T16_4_gblup_variances_all_5001_6000,T16_4_gblup_variances_all_6001_7000,T16_4_gblup_variances_all_7001_8000,T16_4_gblup_variances_all_8001_9000,T16_4_gblup_variances_all_9001_10000,T16_4_gblup_variances_all_10001_11000,T16_4_gblup_variances_all_11001_12419) + +saveRDS(T16_4_gblup_prediction_all,"T16_4_gblup_prediction_all.rds") +saveRDS(T16_4_gblup_variances_all,"T16_4_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_4_gfblup_prediction_all_1_1000=readRDS(file="T16_4_gfblup_prediction_all_1_1000.rds") +T16_4_gfblup_prediction_all_1001_2000=readRDS(file="T16_4_gfblup_prediction_all_1001_2000.rds") +T16_4_gfblup_prediction_all_2001_3000=readRDS(file="T16_4_gfblup_prediction_all_2001_3000.rds") +T16_4_gfblup_prediction_all_3001_4000=readRDS(file="T16_4_gfblup_prediction_all_3001_4000.rds") +T16_4_gfblup_prediction_all_4001_5000=readRDS(file="T16_4_gfblup_prediction_all_4001_5000.rds") +T16_4_gfblup_prediction_all_5001_6000=readRDS(file="T16_4_gfblup_prediction_all_5001_6000.rds") +T16_4_gfblup_prediction_all_6001_7000=readRDS(file="T16_4_gfblup_prediction_all_6001_7000.rds") +T16_4_gfblup_prediction_all_7001_8000=readRDS(file="T16_4_gfblup_prediction_all_7001_8000.rds") +T16_4_gfblup_prediction_all_8001_9000=readRDS(file="T16_4_gfblup_prediction_all_8001_9000.rds") +T16_4_gfblup_prediction_all_9001_10000=readRDS(file="T16_4_gfblup_prediction_all_9001_10000.rds") +T16_4_gfblup_prediction_all_10001_11000=readRDS(file="T16_4_gfblup_prediction_all_10001_11000.rds") +T16_4_gfblup_prediction_all_11001_12419=readRDS(file="T16_4_gfblup_prediction_all_11001_12419.rds") + +T16_4_gfblup_variances_all_1_1000=readRDS(file="T16_4_gfblup_variances_all_1_1000.rds") +T16_4_gfblup_variances_all_1001_2000=readRDS(file="T16_4_gfblup_variances_all_1001_2000.rds") +T16_4_gfblup_variances_all_2001_3000=readRDS(file="T16_4_gfblup_variances_all_2001_3000.rds") +T16_4_gfblup_variances_all_3001_4000=readRDS(file="T16_4_gfblup_variances_all_3001_4000.rds") +T16_4_gfblup_variances_all_4001_5000=readRDS(file="T16_4_gfblup_variances_all_4001_5000.rds") +T16_4_gfblup_variances_all_5001_6000=readRDS(file="T16_4_gfblup_variances_all_5001_6000.rds") +T16_4_gfblup_variances_all_6001_7000=readRDS(file="T16_4_gfblup_variances_all_6001_7000.rds") +T16_4_gfblup_variances_all_7001_8000=readRDS(file="T16_4_gfblup_variances_all_7001_8000.rds") +T16_4_gfblup_variances_all_8001_9000=readRDS(file="T16_4_gfblup_variances_all_8001_9000.rds") +T16_4_gfblup_variances_all_9001_10000=readRDS(file="T16_4_gfblup_variances_all_9001_10000.rds") +T16_4_gfblup_variances_all_10001_11000=readRDS(file="T16_4_gfblup_variances_all_10001_11000.rds") +T16_4_gfblup_variances_all_11001_12419=readRDS(file="T16_4_gfblup_variances_all_11001_12419.rds") + +cycles=length(T16_4_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T16_4_gfblup_variances_all=rep(list(list()),cycles) +T16_4_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_1_1000[[r]]) + T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_1001_2000[[r]]) + T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_2001_3000[[r]]) + T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_3001_4000[[r]]) + T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_4001_5000[[r]]) + T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_5001_6000[[r]]) + T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_6001_7000[[r]]) + T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_7001_8000[[r]]) + T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_8001_9000[[r]]) + T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_9001_10000[[r]]) + T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_10001_11000[[r]]) + T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_11001_12419[[r]]) + + T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_1_1000[[r]]) + T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_1001_2000[[r]]) + T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_2001_3000[[r]]) + T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_3001_4000[[r]]) + T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_4001_5000[[r]]) + T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_5001_6000[[r]]) + T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_6001_7000[[r]]) + T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_7001_8000[[r]]) + T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_8001_9000[[r]]) + T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_9001_10000[[r]]) + T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_10001_11000[[r]]) + T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T16_4_gfblup_prediction_all,"T16_4_gfblup_prediction_all.rds") +saveRDS(T16_4_gfblup_variances_all,"T16_4_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_5_gblup_prediction_all_1_1000=readRDS(file="T16_5_gblup_prediction_all_1_1000.rds") +T16_5_gblup_prediction_all_1001_2000=readRDS(file="T16_5_gblup_prediction_all_1001_2000.rds") +T16_5_gblup_prediction_all_2001_3000=readRDS(file="T16_5_gblup_prediction_all_2001_3000.rds") +T16_5_gblup_prediction_all_3001_4000=readRDS(file="T16_5_gblup_prediction_all_3001_4000.rds") +T16_5_gblup_prediction_all_4001_5000=readRDS(file="T16_5_gblup_prediction_all_4001_5000.rds") +T16_5_gblup_prediction_all_5001_6000=readRDS(file="T16_5_gblup_prediction_all_5001_6000.rds") +T16_5_gblup_prediction_all_6001_7000=readRDS(file="T16_5_gblup_prediction_all_6001_7000.rds") +T16_5_gblup_prediction_all_7001_8000=readRDS(file="T16_5_gblup_prediction_all_7001_8000.rds") +T16_5_gblup_prediction_all_8001_9000=readRDS(file="T16_5_gblup_prediction_all_8001_9000.rds") +T16_5_gblup_prediction_all_9001_10000=readRDS(file="T16_5_gblup_prediction_all_9001_10000.rds") +T16_5_gblup_prediction_all_10001_11000=readRDS(file="T16_5_gblup_prediction_all_10001_11000.rds") +T16_5_gblup_prediction_all_11001_12419=readRDS(file="T16_5_gblup_prediction_all_11001_12419.rds") +T16_5_gblup_prediction_all=c(T16_5_gblup_prediction_all_1_1000,T16_5_gblup_prediction_all_1001_2000,T16_5_gblup_prediction_all_2001_3000,T16_5_gblup_prediction_all_3001_4000,T16_5_gblup_prediction_all_4001_5000,T16_5_gblup_prediction_all_5001_6000,T16_5_gblup_prediction_all_6001_7000,T16_5_gblup_prediction_all_7001_8000,T16_5_gblup_prediction_all_8001_9000,T16_5_gblup_prediction_all_9001_10000,T16_5_gblup_prediction_all_10001_11000,T16_5_gblup_prediction_all_11001_12419) + +T16_5_gblup_variances_all_1_1000=readRDS(file="T16_5_gblup_variances_all_1_1000.rds") +T16_5_gblup_variances_all_1001_2000=readRDS(file="T16_5_gblup_variances_all_1001_2000.rds") +T16_5_gblup_variances_all_2001_3000=readRDS(file="T16_5_gblup_variances_all_2001_3000.rds") +T16_5_gblup_variances_all_3001_4000=readRDS(file="T16_5_gblup_variances_all_3001_4000.rds") +T16_5_gblup_variances_all_4001_5000=readRDS(file="T16_5_gblup_variances_all_4001_5000.rds") +T16_5_gblup_variances_all_5001_6000=readRDS(file="T16_5_gblup_variances_all_5001_6000.rds") +T16_5_gblup_variances_all_6001_7000=readRDS(file="T16_5_gblup_variances_all_6001_7000.rds") +T16_5_gblup_variances_all_7001_8000=readRDS(file="T16_5_gblup_variances_all_7001_8000.rds") +T16_5_gblup_variances_all_8001_9000=readRDS(file="T16_5_gblup_variances_all_8001_9000.rds") +T16_5_gblup_variances_all_9001_10000=readRDS(file="T16_5_gblup_variances_all_9001_10000.rds") +T16_5_gblup_variances_all_10001_11000=readRDS(file="T16_5_gblup_variances_all_10001_11000.rds") +T16_5_gblup_variances_all_11001_12419=readRDS(file="T16_5_gblup_variances_all_11001_12419.rds") +T16_5_gblup_variances_all=c(T16_5_gblup_variances_all_1_1000,T16_5_gblup_variances_all_1001_2000,T16_5_gblup_variances_all_2001_3000,T16_5_gblup_variances_all_3001_4000,T16_5_gblup_variances_all_4001_5000,T16_5_gblup_variances_all_5001_6000,T16_5_gblup_variances_all_6001_7000,T16_5_gblup_variances_all_7001_8000,T16_5_gblup_variances_all_8001_9000,T16_5_gblup_variances_all_9001_10000,T16_5_gblup_variances_all_10001_11000,T16_5_gblup_variances_all_11001_12419) + +saveRDS(T16_5_gblup_prediction_all,"T16_5_gblup_prediction_all.rds") +saveRDS(T16_5_gblup_variances_all,"T16_5_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_5_gfblup_prediction_all_1_1000=readRDS(file="T16_5_gfblup_prediction_all_1_1000.rds") +T16_5_gfblup_prediction_all_1001_2000=readRDS(file="T16_5_gfblup_prediction_all_1001_2000.rds") +T16_5_gfblup_prediction_all_2001_3000=readRDS(file="T16_5_gfblup_prediction_all_2001_3000.rds") +T16_5_gfblup_prediction_all_3001_4000=readRDS(file="T16_5_gfblup_prediction_all_3001_4000.rds") +T16_5_gfblup_prediction_all_4001_5000=readRDS(file="T16_5_gfblup_prediction_all_4001_5000.rds") +T16_5_gfblup_prediction_all_5001_6000=readRDS(file="T16_5_gfblup_prediction_all_5001_6000.rds") +T16_5_gfblup_prediction_all_6001_7000=readRDS(file="T16_5_gfblup_prediction_all_6001_7000.rds") +T16_5_gfblup_prediction_all_7001_8000=readRDS(file="T16_5_gfblup_prediction_all_7001_8000.rds") +T16_5_gfblup_prediction_all_8001_9000=readRDS(file="T16_5_gfblup_prediction_all_8001_9000.rds") +T16_5_gfblup_prediction_all_9001_10000=readRDS(file="T16_5_gfblup_prediction_all_9001_10000.rds") +T16_5_gfblup_prediction_all_10001_11000=readRDS(file="T16_5_gfblup_prediction_all_10001_11000.rds") +T16_5_gfblup_prediction_all_11001_12419=readRDS(file="T16_5_gfblup_prediction_all_11001_12419.rds") + +T16_5_gfblup_variances_all_1_1000=readRDS(file="T16_5_gfblup_variances_all_1_1000.rds") +T16_5_gfblup_variances_all_1001_2000=readRDS(file="T16_5_gfblup_variances_all_1001_2000.rds") +T16_5_gfblup_variances_all_2001_3000=readRDS(file="T16_5_gfblup_variances_all_2001_3000.rds") +T16_5_gfblup_variances_all_3001_4000=readRDS(file="T16_5_gfblup_variances_all_3001_4000.rds") +T16_5_gfblup_variances_all_4001_5000=readRDS(file="T16_5_gfblup_variances_all_4001_5000.rds") +T16_5_gfblup_variances_all_5001_6000=readRDS(file="T16_5_gfblup_variances_all_5001_6000.rds") +T16_5_gfblup_variances_all_6001_7000=readRDS(file="T16_5_gfblup_variances_all_6001_7000.rds") +T16_5_gfblup_variances_all_7001_8000=readRDS(file="T16_5_gfblup_variances_all_7001_8000.rds") +T16_5_gfblup_variances_all_8001_9000=readRDS(file="T16_5_gfblup_variances_all_8001_9000.rds") +T16_5_gfblup_variances_all_9001_10000=readRDS(file="T16_5_gfblup_variances_all_9001_10000.rds") +T16_5_gfblup_variances_all_10001_11000=readRDS(file="T16_5_gfblup_variances_all_10001_11000.rds") +T16_5_gfblup_variances_all_11001_12419=readRDS(file="T16_5_gfblup_variances_all_11001_12419.rds") + +cycles=length(T16_5_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T16_5_gfblup_variances_all=rep(list(list()),cycles) +T16_5_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_1_1000[[r]]) + T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_1001_2000[[r]]) + T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_2001_3000[[r]]) + T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_3001_4000[[r]]) + T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_4001_5000[[r]]) + T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_5001_6000[[r]]) + T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_6001_7000[[r]]) + T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_7001_8000[[r]]) + T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_8001_9000[[r]]) + T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_9001_10000[[r]]) + T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_10001_11000[[r]]) + T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_11001_12419[[r]]) + + T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_1_1000[[r]]) + T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_1001_2000[[r]]) + T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_2001_3000[[r]]) + T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_3001_4000[[r]]) + T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_4001_5000[[r]]) + T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_5001_6000[[r]]) + T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_6001_7000[[r]]) + T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_7001_8000[[r]]) + T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_8001_9000[[r]]) + T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_9001_10000[[r]]) + T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_10001_11000[[r]]) + T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T16_5_gfblup_prediction_all,"T16_5_gfblup_prediction_all.rds") +saveRDS(T16_5_gfblup_variances_all,"T16_5_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_6_gblup_prediction_all_1_1000=readRDS(file="T16_6_gblup_prediction_all_1_1000.rds") +T16_6_gblup_prediction_all_1001_2000=readRDS(file="T16_6_gblup_prediction_all_1001_2000.rds") +T16_6_gblup_prediction_all_2001_3000=readRDS(file="T16_6_gblup_prediction_all_2001_3000.rds") +T16_6_gblup_prediction_all_3001_4000=readRDS(file="T16_6_gblup_prediction_all_3001_4000.rds") +T16_6_gblup_prediction_all_4001_5000=readRDS(file="T16_6_gblup_prediction_all_4001_5000.rds") +T16_6_gblup_prediction_all_5001_6000=readRDS(file="T16_6_gblup_prediction_all_5001_6000.rds") +T16_6_gblup_prediction_all_6001_7000=readRDS(file="T16_6_gblup_prediction_all_6001_7000.rds") +T16_6_gblup_prediction_all_7001_8000=readRDS(file="T16_6_gblup_prediction_all_7001_8000.rds") +T16_6_gblup_prediction_all_8001_9000=readRDS(file="T16_6_gblup_prediction_all_8001_9000.rds") +T16_6_gblup_prediction_all_9001_10000=readRDS(file="T16_6_gblup_prediction_all_9001_10000.rds") +T16_6_gblup_prediction_all_10001_11000=readRDS(file="T16_6_gblup_prediction_all_10001_11000.rds") +T16_6_gblup_prediction_all_11001_12419=readRDS(file="T16_6_gblup_prediction_all_11001_12419.rds") +T16_6_gblup_prediction_all=c(T16_6_gblup_prediction_all_1_1000,T16_6_gblup_prediction_all_1001_2000,T16_6_gblup_prediction_all_2001_3000,T16_6_gblup_prediction_all_3001_4000,T16_6_gblup_prediction_all_4001_5000,T16_6_gblup_prediction_all_5001_6000,T16_6_gblup_prediction_all_6001_7000,T16_6_gblup_prediction_all_7001_8000,T16_6_gblup_prediction_all_8001_9000,T16_6_gblup_prediction_all_9001_10000,T16_6_gblup_prediction_all_10001_11000,T16_6_gblup_prediction_all_11001_12419) + +T16_6_gblup_variances_all_1_1000=readRDS(file="T16_6_gblup_variances_all_1_1000.rds") +T16_6_gblup_variances_all_1001_2000=readRDS(file="T16_6_gblup_variances_all_1001_2000.rds") +T16_6_gblup_variances_all_2001_3000=readRDS(file="T16_6_gblup_variances_all_2001_3000.rds") +T16_6_gblup_variances_all_3001_4000=readRDS(file="T16_6_gblup_variances_all_3001_4000.rds") +T16_6_gblup_variances_all_4001_5000=readRDS(file="T16_6_gblup_variances_all_4001_5000.rds") +T16_6_gblup_variances_all_5001_6000=readRDS(file="T16_6_gblup_variances_all_5001_6000.rds") +T16_6_gblup_variances_all_6001_7000=readRDS(file="T16_6_gblup_variances_all_6001_7000.rds") +T16_6_gblup_variances_all_7001_8000=readRDS(file="T16_6_gblup_variances_all_7001_8000.rds") +T16_6_gblup_variances_all_8001_9000=readRDS(file="T16_6_gblup_variances_all_8001_9000.rds") +T16_6_gblup_variances_all_9001_10000=readRDS(file="T16_6_gblup_variances_all_9001_10000.rds") +T16_6_gblup_variances_all_10001_11000=readRDS(file="T16_6_gblup_variances_all_10001_11000.rds") +T16_6_gblup_variances_all_11001_12419=readRDS(file="T16_6_gblup_variances_all_11001_12419.rds") +T16_6_gblup_variances_all=c(T16_6_gblup_variances_all_1_1000,T16_6_gblup_variances_all_1001_2000,T16_6_gblup_variances_all_2001_3000,T16_6_gblup_variances_all_3001_4000,T16_6_gblup_variances_all_4001_5000,T16_6_gblup_variances_all_5001_6000,T16_6_gblup_variances_all_6001_7000,T16_6_gblup_variances_all_7001_8000,T16_6_gblup_variances_all_8001_9000,T16_6_gblup_variances_all_9001_10000,T16_6_gblup_variances_all_10001_11000,T16_6_gblup_variances_all_11001_12419) + +saveRDS(T16_6_gblup_prediction_all,"T16_6_gblup_prediction_all.rds") +saveRDS(T16_6_gblup_variances_all,"T16_6_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_6_gfblup_prediction_all_1_1000=readRDS(file="T16_6_gfblup_prediction_all_1_1000.rds") +T16_6_gfblup_prediction_all_1001_2000=readRDS(file="T16_6_gfblup_prediction_all_1001_2000.rds") +T16_6_gfblup_prediction_all_2001_3000=readRDS(file="T16_6_gfblup_prediction_all_2001_3000.rds") +T16_6_gfblup_prediction_all_3001_4000=readRDS(file="T16_6_gfblup_prediction_all_3001_4000.rds") +T16_6_gfblup_prediction_all_4001_5000=readRDS(file="T16_6_gfblup_prediction_all_4001_5000.rds") +T16_6_gfblup_prediction_all_5001_6000=readRDS(file="T16_6_gfblup_prediction_all_5001_6000.rds") +T16_6_gfblup_prediction_all_6001_7000=readRDS(file="T16_6_gfblup_prediction_all_6001_7000.rds") +T16_6_gfblup_prediction_all_7001_8000=readRDS(file="T16_6_gfblup_prediction_all_7001_8000.rds") +T16_6_gfblup_prediction_all_8001_9000=readRDS(file="T16_6_gfblup_prediction_all_8001_9000.rds") +T16_6_gfblup_prediction_all_9001_10000=readRDS(file="T16_6_gfblup_prediction_all_9001_10000.rds") +T16_6_gfblup_prediction_all_10001_11000=readRDS(file="T16_6_gfblup_prediction_all_10001_11000.rds") +T16_6_gfblup_prediction_all_11001_12419=readRDS(file="T16_6_gfblup_prediction_all_11001_12419.rds") + +T16_6_gfblup_variances_all_1_1000=readRDS(file="T16_6_gfblup_variances_all_1_1000.rds") +T16_6_gfblup_variances_all_1001_2000=readRDS(file="T16_6_gfblup_variances_all_1001_2000.rds") +T16_6_gfblup_variances_all_2001_3000=readRDS(file="T16_6_gfblup_variances_all_2001_3000.rds") +T16_6_gfblup_variances_all_3001_4000=readRDS(file="T16_6_gfblup_variances_all_3001_4000.rds") +T16_6_gfblup_variances_all_4001_5000=readRDS(file="T16_6_gfblup_variances_all_4001_5000.rds") +T16_6_gfblup_variances_all_5001_6000=readRDS(file="T16_6_gfblup_variances_all_5001_6000.rds") +T16_6_gfblup_variances_all_6001_7000=readRDS(file="T16_6_gfblup_variances_all_6001_7000.rds") +T16_6_gfblup_variances_all_7001_8000=readRDS(file="T16_6_gfblup_variances_all_7001_8000.rds") +T16_6_gfblup_variances_all_8001_9000=readRDS(file="T16_6_gfblup_variances_all_8001_9000.rds") +T16_6_gfblup_variances_all_9001_10000=readRDS(file="T16_6_gfblup_variances_all_9001_10000.rds") +T16_6_gfblup_variances_all_10001_11000=readRDS(file="T16_6_gfblup_variances_all_10001_11000.rds") +T16_6_gfblup_variances_all_11001_12419=readRDS(file="T16_6_gfblup_variances_all_11001_12419.rds") + +cycles=length(T16_6_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T16_6_gfblup_variances_all=rep(list(list()),cycles) +T16_6_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_1_1000[[r]]) + T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_1001_2000[[r]]) + T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_2001_3000[[r]]) + T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_3001_4000[[r]]) + T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_4001_5000[[r]]) + T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_5001_6000[[r]]) + T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_6001_7000[[r]]) + T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_7001_8000[[r]]) + T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_8001_9000[[r]]) + T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_9001_10000[[r]]) + T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_10001_11000[[r]]) + T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_11001_12419[[r]]) + + T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_1_1000[[r]]) + T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_1001_2000[[r]]) + T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_2001_3000[[r]]) + T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_3001_4000[[r]]) + T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_4001_5000[[r]]) + T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_5001_6000[[r]]) + T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_6001_7000[[r]]) + T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_7001_8000[[r]]) + T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_8001_9000[[r]]) + T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_9001_10000[[r]]) + T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_10001_11000[[r]]) + T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T16_6_gfblup_prediction_all,"T16_6_gfblup_prediction_all.rds") +saveRDS(T16_6_gfblup_variances_all,"T16_6_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_7_gblup_prediction_all_1_1000=readRDS(file="T16_7_gblup_prediction_all_1_1000.rds") +T16_7_gblup_prediction_all_1001_2000=readRDS(file="T16_7_gblup_prediction_all_1001_2000.rds") +T16_7_gblup_prediction_all_2001_3000=readRDS(file="T16_7_gblup_prediction_all_2001_3000.rds") +T16_7_gblup_prediction_all_3001_4000=readRDS(file="T16_7_gblup_prediction_all_3001_4000.rds") +T16_7_gblup_prediction_all_4001_5000=readRDS(file="T16_7_gblup_prediction_all_4001_5000.rds") +T16_7_gblup_prediction_all_5001_6000=readRDS(file="T16_7_gblup_prediction_all_5001_6000.rds") +T16_7_gblup_prediction_all_6001_7000=readRDS(file="T16_7_gblup_prediction_all_6001_7000.rds") +T16_7_gblup_prediction_all_7001_8000=readRDS(file="T16_7_gblup_prediction_all_7001_8000.rds") +T16_7_gblup_prediction_all_8001_9000=readRDS(file="T16_7_gblup_prediction_all_8001_9000.rds") +T16_7_gblup_prediction_all_9001_10000=readRDS(file="T16_7_gblup_prediction_all_9001_10000.rds") +T16_7_gblup_prediction_all_10001_11000=readRDS(file="T16_7_gblup_prediction_all_10001_11000.rds") +T16_7_gblup_prediction_all_11001_12419=readRDS(file="T16_7_gblup_prediction_all_11001_12419.rds") +T16_7_gblup_prediction_all=c(T16_7_gblup_prediction_all_1_1000,T16_7_gblup_prediction_all_1001_2000,T16_7_gblup_prediction_all_2001_3000,T16_7_gblup_prediction_all_3001_4000,T16_7_gblup_prediction_all_4001_5000,T16_7_gblup_prediction_all_5001_6000,T16_7_gblup_prediction_all_6001_7000,T16_7_gblup_prediction_all_7001_8000,T16_7_gblup_prediction_all_8001_9000,T16_7_gblup_prediction_all_9001_10000,T16_7_gblup_prediction_all_10001_11000,T16_7_gblup_prediction_all_11001_12419) + +T16_7_gblup_variances_all_1_1000=readRDS(file="T16_7_gblup_variances_all_1_1000.rds") +T16_7_gblup_variances_all_1001_2000=readRDS(file="T16_7_gblup_variances_all_1001_2000.rds") +T16_7_gblup_variances_all_2001_3000=readRDS(file="T16_7_gblup_variances_all_2001_3000.rds") +T16_7_gblup_variances_all_3001_4000=readRDS(file="T16_7_gblup_variances_all_3001_4000.rds") +T16_7_gblup_variances_all_4001_5000=readRDS(file="T16_7_gblup_variances_all_4001_5000.rds") +T16_7_gblup_variances_all_5001_6000=readRDS(file="T16_7_gblup_variances_all_5001_6000.rds") +T16_7_gblup_variances_all_6001_7000=readRDS(file="T16_7_gblup_variances_all_6001_7000.rds") +T16_7_gblup_variances_all_7001_8000=readRDS(file="T16_7_gblup_variances_all_7001_8000.rds") +T16_7_gblup_variances_all_8001_9000=readRDS(file="T16_7_gblup_variances_all_8001_9000.rds") +T16_7_gblup_variances_all_9001_10000=readRDS(file="T16_7_gblup_variances_all_9001_10000.rds") +T16_7_gblup_variances_all_10001_11000=readRDS(file="T16_7_gblup_variances_all_10001_11000.rds") +T16_7_gblup_variances_all_11001_12419=readRDS(file="T16_7_gblup_variances_all_11001_12419.rds") +T16_7_gblup_variances_all=c(T16_7_gblup_variances_all_1_1000,T16_7_gblup_variances_all_1001_2000,T16_7_gblup_variances_all_2001_3000,T16_7_gblup_variances_all_3001_4000,T16_7_gblup_variances_all_4001_5000,T16_7_gblup_variances_all_5001_6000,T16_7_gblup_variances_all_6001_7000,T16_7_gblup_variances_all_7001_8000,T16_7_gblup_variances_all_8001_9000,T16_7_gblup_variances_all_9001_10000,T16_7_gblup_variances_all_10001_11000,T16_7_gblup_variances_all_11001_12419) + +saveRDS(T16_7_gblup_prediction_all,"T16_7_gblup_prediction_all.rds") +saveRDS(T16_7_gblup_variances_all,"T16_7_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_7_gfblup_prediction_all_1_1000=readRDS(file="T16_7_gfblup_prediction_all_1_1000.rds") +T16_7_gfblup_prediction_all_1001_2000=readRDS(file="T16_7_gfblup_prediction_all_1001_2000.rds") +T16_7_gfblup_prediction_all_2001_3000=readRDS(file="T16_7_gfblup_prediction_all_2001_3000.rds") +T16_7_gfblup_prediction_all_3001_4000=readRDS(file="T16_7_gfblup_prediction_all_3001_4000.rds") +T16_7_gfblup_prediction_all_4001_5000=readRDS(file="T16_7_gfblup_prediction_all_4001_5000.rds") +T16_7_gfblup_prediction_all_5001_6000=readRDS(file="T16_7_gfblup_prediction_all_5001_6000.rds") +T16_7_gfblup_prediction_all_6001_7000=readRDS(file="T16_7_gfblup_prediction_all_6001_7000.rds") +T16_7_gfblup_prediction_all_7001_8000=readRDS(file="T16_7_gfblup_prediction_all_7001_8000.rds") +T16_7_gfblup_prediction_all_8001_9000=readRDS(file="T16_7_gfblup_prediction_all_8001_9000.rds") +T16_7_gfblup_prediction_all_9001_10000=readRDS(file="T16_7_gfblup_prediction_all_9001_10000.rds") +T16_7_gfblup_prediction_all_10001_11000=readRDS(file="T16_7_gfblup_prediction_all_10001_11000.rds") +T16_7_gfblup_prediction_all_11001_12419=readRDS(file="T16_7_gfblup_prediction_all_11001_12419.rds") + +T16_7_gfblup_variances_all_1_1000=readRDS(file="T16_7_gfblup_variances_all_1_1000.rds") +T16_7_gfblup_variances_all_1001_2000=readRDS(file="T16_7_gfblup_variances_all_1001_2000.rds") +T16_7_gfblup_variances_all_2001_3000=readRDS(file="T16_7_gfblup_variances_all_2001_3000.rds") +T16_7_gfblup_variances_all_3001_4000=readRDS(file="T16_7_gfblup_variances_all_3001_4000.rds") +T16_7_gfblup_variances_all_4001_5000=readRDS(file="T16_7_gfblup_variances_all_4001_5000.rds") +T16_7_gfblup_variances_all_5001_6000=readRDS(file="T16_7_gfblup_variances_all_5001_6000.rds") +T16_7_gfblup_variances_all_6001_7000=readRDS(file="T16_7_gfblup_variances_all_6001_7000.rds") +T16_7_gfblup_variances_all_7001_8000=readRDS(file="T16_7_gfblup_variances_all_7001_8000.rds") +T16_7_gfblup_variances_all_8001_9000=readRDS(file="T16_7_gfblup_variances_all_8001_9000.rds") +T16_7_gfblup_variances_all_9001_10000=readRDS(file="T16_7_gfblup_variances_all_9001_10000.rds") +T16_7_gfblup_variances_all_10001_11000=readRDS(file="T16_7_gfblup_variances_all_10001_11000.rds") +T16_7_gfblup_variances_all_11001_12419=readRDS(file="T16_7_gfblup_variances_all_11001_12419.rds") + +cycles=length(T16_7_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T16_7_gfblup_variances_all=rep(list(list()),cycles) +T16_7_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_1_1000[[r]]) + T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_1001_2000[[r]]) + T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_2001_3000[[r]]) + T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_3001_4000[[r]]) + T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_4001_5000[[r]]) + T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_5001_6000[[r]]) + T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_6001_7000[[r]]) + T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_7001_8000[[r]]) + T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_8001_9000[[r]]) + T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_9001_10000[[r]]) + T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_10001_11000[[r]]) + T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_11001_12419[[r]]) + + T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_1_1000[[r]]) + T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_1001_2000[[r]]) + T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_2001_3000[[r]]) + T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_3001_4000[[r]]) + T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_4001_5000[[r]]) + T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_5001_6000[[r]]) + T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_6001_7000[[r]]) + T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_7001_8000[[r]]) + T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_8001_9000[[r]]) + T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_9001_10000[[r]]) + T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_10001_11000[[r]]) + T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T16_7_gfblup_prediction_all,"T16_7_gfblup_prediction_all.rds") +saveRDS(T16_7_gfblup_variances_all,"T16_7_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_8_gblup_prediction_all_1_1000=readRDS(file="T16_8_gblup_prediction_all_1_1000.rds") +T16_8_gblup_prediction_all_1001_2000=readRDS(file="T16_8_gblup_prediction_all_1001_2000.rds") +T16_8_gblup_prediction_all_2001_3000=readRDS(file="T16_8_gblup_prediction_all_2001_3000.rds") +T16_8_gblup_prediction_all_3001_4000=readRDS(file="T16_8_gblup_prediction_all_3001_4000.rds") +T16_8_gblup_prediction_all_4001_5000=readRDS(file="T16_8_gblup_prediction_all_4001_5000.rds") +T16_8_gblup_prediction_all_5001_6000=readRDS(file="T16_8_gblup_prediction_all_5001_6000.rds") +T16_8_gblup_prediction_all_6001_7000=readRDS(file="T16_8_gblup_prediction_all_6001_7000.rds") +T16_8_gblup_prediction_all_7001_8000=readRDS(file="T16_8_gblup_prediction_all_7001_8000.rds") +T16_8_gblup_prediction_all_8001_9000=readRDS(file="T16_8_gblup_prediction_all_8001_9000.rds") +T16_8_gblup_prediction_all_9001_10000=readRDS(file="T16_8_gblup_prediction_all_9001_10000.rds") +T16_8_gblup_prediction_all_10001_11000=readRDS(file="T16_8_gblup_prediction_all_10001_11000.rds") +T16_8_gblup_prediction_all_11001_12419=readRDS(file="T16_8_gblup_prediction_all_11001_12419.rds") +T16_8_gblup_prediction_all=c(T16_8_gblup_prediction_all_1_1000,T16_8_gblup_prediction_all_1001_2000,T16_8_gblup_prediction_all_2001_3000,T16_8_gblup_prediction_all_3001_4000,T16_8_gblup_prediction_all_4001_5000,T16_8_gblup_prediction_all_5001_6000,T16_8_gblup_prediction_all_6001_7000,T16_8_gblup_prediction_all_7001_8000,T16_8_gblup_prediction_all_8001_9000,T16_8_gblup_prediction_all_9001_10000,T16_8_gblup_prediction_all_10001_11000,T16_8_gblup_prediction_all_11001_12419) + +T16_8_gblup_variances_all_1_1000=readRDS(file="T16_8_gblup_variances_all_1_1000.rds") +T16_8_gblup_variances_all_1001_2000=readRDS(file="T16_8_gblup_variances_all_1001_2000.rds") +T16_8_gblup_variances_all_2001_3000=readRDS(file="T16_8_gblup_variances_all_2001_3000.rds") +T16_8_gblup_variances_all_3001_4000=readRDS(file="T16_8_gblup_variances_all_3001_4000.rds") +T16_8_gblup_variances_all_4001_5000=readRDS(file="T16_8_gblup_variances_all_4001_5000.rds") +T16_8_gblup_variances_all_5001_6000=readRDS(file="T16_8_gblup_variances_all_5001_6000.rds") +T16_8_gblup_variances_all_6001_7000=readRDS(file="T16_8_gblup_variances_all_6001_7000.rds") +T16_8_gblup_variances_all_7001_8000=readRDS(file="T16_8_gblup_variances_all_7001_8000.rds") +T16_8_gblup_variances_all_8001_9000=readRDS(file="T16_8_gblup_variances_all_8001_9000.rds") +T16_8_gblup_variances_all_9001_10000=readRDS(file="T16_8_gblup_variances_all_9001_10000.rds") +T16_8_gblup_variances_all_10001_11000=readRDS(file="T16_8_gblup_variances_all_10001_11000.rds") +T16_8_gblup_variances_all_11001_12419=readRDS(file="T16_8_gblup_variances_all_11001_12419.rds") +T16_8_gblup_variances_all=c(T16_8_gblup_variances_all_1_1000,T16_8_gblup_variances_all_1001_2000,T16_8_gblup_variances_all_2001_3000,T16_8_gblup_variances_all_3001_4000,T16_8_gblup_variances_all_4001_5000,T16_8_gblup_variances_all_5001_6000,T16_8_gblup_variances_all_6001_7000,T16_8_gblup_variances_all_7001_8000,T16_8_gblup_variances_all_8001_9000,T16_8_gblup_variances_all_9001_10000,T16_8_gblup_variances_all_10001_11000,T16_8_gblup_variances_all_11001_12419) + +saveRDS(T16_8_gblup_prediction_all,"T16_8_gblup_prediction_all.rds") +saveRDS(T16_8_gblup_variances_all,"T16_8_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_8_gfblup_prediction_all_1_1000=readRDS(file="T16_8_gfblup_prediction_all_1_1000.rds") +T16_8_gfblup_prediction_all_1001_2000=readRDS(file="T16_8_gfblup_prediction_all_1001_2000.rds") +T16_8_gfblup_prediction_all_2001_3000=readRDS(file="T16_8_gfblup_prediction_all_2001_3000.rds") +T16_8_gfblup_prediction_all_3001_4000=readRDS(file="T16_8_gfblup_prediction_all_3001_4000.rds") +T16_8_gfblup_prediction_all_4001_5000=readRDS(file="T16_8_gfblup_prediction_all_4001_5000.rds") +T16_8_gfblup_prediction_all_5001_6000=readRDS(file="T16_8_gfblup_prediction_all_5001_6000.rds") +T16_8_gfblup_prediction_all_6001_7000=readRDS(file="T16_8_gfblup_prediction_all_6001_7000.rds") +T16_8_gfblup_prediction_all_7001_8000=readRDS(file="T16_8_gfblup_prediction_all_7001_8000.rds") +T16_8_gfblup_prediction_all_8001_9000=readRDS(file="T16_8_gfblup_prediction_all_8001_9000.rds") +T16_8_gfblup_prediction_all_9001_10000=readRDS(file="T16_8_gfblup_prediction_all_9001_10000.rds") +T16_8_gfblup_prediction_all_10001_11000=readRDS(file="T16_8_gfblup_prediction_all_10001_11000.rds") +T16_8_gfblup_prediction_all_11001_12419=readRDS(file="T16_8_gfblup_prediction_all_11001_12419.rds") + +T16_8_gfblup_variances_all_1_1000=readRDS(file="T16_8_gfblup_variances_all_1_1000.rds") +T16_8_gfblup_variances_all_1001_2000=readRDS(file="T16_8_gfblup_variances_all_1001_2000.rds") +T16_8_gfblup_variances_all_2001_3000=readRDS(file="T16_8_gfblup_variances_all_2001_3000.rds") +T16_8_gfblup_variances_all_3001_4000=readRDS(file="T16_8_gfblup_variances_all_3001_4000.rds") +T16_8_gfblup_variances_all_4001_5000=readRDS(file="T16_8_gfblup_variances_all_4001_5000.rds") +T16_8_gfblup_variances_all_5001_6000=readRDS(file="T16_8_gfblup_variances_all_5001_6000.rds") +T16_8_gfblup_variances_all_6001_7000=readRDS(file="T16_8_gfblup_variances_all_6001_7000.rds") +T16_8_gfblup_variances_all_7001_8000=readRDS(file="T16_8_gfblup_variances_all_7001_8000.rds") +T16_8_gfblup_variances_all_8001_9000=readRDS(file="T16_8_gfblup_variances_all_8001_9000.rds") +T16_8_gfblup_variances_all_9001_10000=readRDS(file="T16_8_gfblup_variances_all_9001_10000.rds") +T16_8_gfblup_variances_all_10001_11000=readRDS(file="T16_8_gfblup_variances_all_10001_11000.rds") +T16_8_gfblup_variances_all_11001_12419=readRDS(file="T16_8_gfblup_variances_all_11001_12419.rds") + +cycles=length(T16_8_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T16_8_gfblup_variances_all=rep(list(list()),cycles) +T16_8_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_1_1000[[r]]) + T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_1001_2000[[r]]) + T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_2001_3000[[r]]) + T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_3001_4000[[r]]) + T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_4001_5000[[r]]) + T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_5001_6000[[r]]) + T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_6001_7000[[r]]) + T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_7001_8000[[r]]) + T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_8001_9000[[r]]) + T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_9001_10000[[r]]) + T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_10001_11000[[r]]) + T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_11001_12419[[r]]) + + T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_1_1000[[r]]) + T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_1001_2000[[r]]) + T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_2001_3000[[r]]) + T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_3001_4000[[r]]) + T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_4001_5000[[r]]) + T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_5001_6000[[r]]) + T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_6001_7000[[r]]) + T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_7001_8000[[r]]) + T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_8001_9000[[r]]) + T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_9001_10000[[r]]) + T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_10001_11000[[r]]) + T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T16_8_gfblup_prediction_all,"T16_8_gfblup_prediction_all.rds") +saveRDS(T16_8_gfblup_variances_all,"T16_8_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_1_gblup_prediction_all_1_1000=readRDS(file="T17_1_gblup_prediction_all_1_1000.rds") +T17_1_gblup_prediction_all_1001_2000=readRDS(file="T17_1_gblup_prediction_all_1001_2000.rds") +T17_1_gblup_prediction_all_2001_3000=readRDS(file="T17_1_gblup_prediction_all_2001_3000.rds") +T17_1_gblup_prediction_all_3001_4000=readRDS(file="T17_1_gblup_prediction_all_3001_4000.rds") +T17_1_gblup_prediction_all_4001_5000=readRDS(file="T17_1_gblup_prediction_all_4001_5000.rds") +T17_1_gblup_prediction_all_5001_6000=readRDS(file="T17_1_gblup_prediction_all_5001_6000.rds") +T17_1_gblup_prediction_all_6001_7000=readRDS(file="T17_1_gblup_prediction_all_6001_7000.rds") +T17_1_gblup_prediction_all_7001_8000=readRDS(file="T17_1_gblup_prediction_all_7001_8000.rds") +T17_1_gblup_prediction_all_8001_9000=readRDS(file="T17_1_gblup_prediction_all_8001_9000.rds") +T17_1_gblup_prediction_all_9001_10000=readRDS(file="T17_1_gblup_prediction_all_9001_10000.rds") +T17_1_gblup_prediction_all_10001_11000=readRDS(file="T17_1_gblup_prediction_all_10001_11000.rds") +T17_1_gblup_prediction_all_11001_12419=readRDS(file="T17_1_gblup_prediction_all_11001_12419.rds") +T17_1_gblup_prediction_all=c(T17_1_gblup_prediction_all_1_1000,T17_1_gblup_prediction_all_1001_2000,T17_1_gblup_prediction_all_2001_3000,T17_1_gblup_prediction_all_3001_4000,T17_1_gblup_prediction_all_4001_5000,T17_1_gblup_prediction_all_5001_6000,T17_1_gblup_prediction_all_6001_7000,T17_1_gblup_prediction_all_7001_8000,T17_1_gblup_prediction_all_8001_9000,T17_1_gblup_prediction_all_9001_10000,T17_1_gblup_prediction_all_10001_11000,T17_1_gblup_prediction_all_11001_12419) + +T17_1_gblup_variances_all_1_1000=readRDS(file="T17_1_gblup_variances_all_1_1000.rds") +T17_1_gblup_variances_all_1001_2000=readRDS(file="T17_1_gblup_variances_all_1001_2000.rds") +T17_1_gblup_variances_all_2001_3000=readRDS(file="T17_1_gblup_variances_all_2001_3000.rds") +T17_1_gblup_variances_all_3001_4000=readRDS(file="T17_1_gblup_variances_all_3001_4000.rds") +T17_1_gblup_variances_all_4001_5000=readRDS(file="T17_1_gblup_variances_all_4001_5000.rds") +T17_1_gblup_variances_all_5001_6000=readRDS(file="T17_1_gblup_variances_all_5001_6000.rds") +T17_1_gblup_variances_all_6001_7000=readRDS(file="T17_1_gblup_variances_all_6001_7000.rds") +T17_1_gblup_variances_all_7001_8000=readRDS(file="T17_1_gblup_variances_all_7001_8000.rds") +T17_1_gblup_variances_all_8001_9000=readRDS(file="T17_1_gblup_variances_all_8001_9000.rds") +T17_1_gblup_variances_all_9001_10000=readRDS(file="T17_1_gblup_variances_all_9001_10000.rds") +T17_1_gblup_variances_all_10001_11000=readRDS(file="T17_1_gblup_variances_all_10001_11000.rds") +T17_1_gblup_variances_all_11001_12419=readRDS(file="T17_1_gblup_variances_all_11001_12419.rds") +T17_1_gblup_variances_all=c(T17_1_gblup_variances_all_1_1000,T17_1_gblup_variances_all_1001_2000,T17_1_gblup_variances_all_2001_3000,T17_1_gblup_variances_all_3001_4000,T17_1_gblup_variances_all_4001_5000,T17_1_gblup_variances_all_5001_6000,T17_1_gblup_variances_all_6001_7000,T17_1_gblup_variances_all_7001_8000,T17_1_gblup_variances_all_8001_9000,T17_1_gblup_variances_all_9001_10000,T17_1_gblup_variances_all_10001_11000,T17_1_gblup_variances_all_11001_12419) + +saveRDS(T17_1_gblup_prediction_all,"T17_1_gblup_prediction_all.rds") +saveRDS(T17_1_gblup_variances_all,"T17_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_1_gfblup_prediction_all_1_1000=readRDS(file="T17_1_gfblup_prediction_all_1_1000.rds") +T17_1_gfblup_prediction_all_1001_2000=readRDS(file="T17_1_gfblup_prediction_all_1001_2000.rds") +T17_1_gfblup_prediction_all_2001_3000=readRDS(file="T17_1_gfblup_prediction_all_2001_3000.rds") +T17_1_gfblup_prediction_all_3001_4000=readRDS(file="T17_1_gfblup_prediction_all_3001_4000.rds") +T17_1_gfblup_prediction_all_4001_5000=readRDS(file="T17_1_gfblup_prediction_all_4001_5000.rds") +T17_1_gfblup_prediction_all_5001_6000=readRDS(file="T17_1_gfblup_prediction_all_5001_6000.rds") +T17_1_gfblup_prediction_all_6001_7000=readRDS(file="T17_1_gfblup_prediction_all_6001_7000.rds") +T17_1_gfblup_prediction_all_7001_8000=readRDS(file="T17_1_gfblup_prediction_all_7001_8000.rds") +T17_1_gfblup_prediction_all_8001_9000=readRDS(file="T17_1_gfblup_prediction_all_8001_9000.rds") +T17_1_gfblup_prediction_all_9001_10000=readRDS(file="T17_1_gfblup_prediction_all_9001_10000.rds") +T17_1_gfblup_prediction_all_10001_11000=readRDS(file="T17_1_gfblup_prediction_all_10001_11000.rds") +T17_1_gfblup_prediction_all_11001_12419=readRDS(file="T17_1_gfblup_prediction_all_11001_12419.rds") + +T17_1_gfblup_variances_all_1_1000=readRDS(file="T17_1_gfblup_variances_all_1_1000.rds") +T17_1_gfblup_variances_all_1001_2000=readRDS(file="T17_1_gfblup_variances_all_1001_2000.rds") +T17_1_gfblup_variances_all_2001_3000=readRDS(file="T17_1_gfblup_variances_all_2001_3000.rds") +T17_1_gfblup_variances_all_3001_4000=readRDS(file="T17_1_gfblup_variances_all_3001_4000.rds") +T17_1_gfblup_variances_all_4001_5000=readRDS(file="T17_1_gfblup_variances_all_4001_5000.rds") +T17_1_gfblup_variances_all_5001_6000=readRDS(file="T17_1_gfblup_variances_all_5001_6000.rds") +T17_1_gfblup_variances_all_6001_7000=readRDS(file="T17_1_gfblup_variances_all_6001_7000.rds") +T17_1_gfblup_variances_all_7001_8000=readRDS(file="T17_1_gfblup_variances_all_7001_8000.rds") +T17_1_gfblup_variances_all_8001_9000=readRDS(file="T17_1_gfblup_variances_all_8001_9000.rds") +T17_1_gfblup_variances_all_9001_10000=readRDS(file="T17_1_gfblup_variances_all_9001_10000.rds") +T17_1_gfblup_variances_all_10001_11000=readRDS(file="T17_1_gfblup_variances_all_10001_11000.rds") +T17_1_gfblup_variances_all_11001_12419=readRDS(file="T17_1_gfblup_variances_all_11001_12419.rds") + +cycles=length(T17_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T17_1_gfblup_variances_all=rep(list(list()),cycles) +T17_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_1_1000[[r]]) + T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_1001_2000[[r]]) + T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_2001_3000[[r]]) + T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_3001_4000[[r]]) + T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_4001_5000[[r]]) + T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_5001_6000[[r]]) + T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_6001_7000[[r]]) + T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_7001_8000[[r]]) + T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_8001_9000[[r]]) + T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_9001_10000[[r]]) + T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_10001_11000[[r]]) + T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_11001_12419[[r]]) + + T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_1_1000[[r]]) + T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_1001_2000[[r]]) + T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_2001_3000[[r]]) + T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_3001_4000[[r]]) + T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_4001_5000[[r]]) + T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_5001_6000[[r]]) + T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_6001_7000[[r]]) + T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_7001_8000[[r]]) + T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_8001_9000[[r]]) + T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_9001_10000[[r]]) + T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_10001_11000[[r]]) + T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T17_1_gfblup_prediction_all,"T17_1_gfblup_prediction_all.rds") +saveRDS(T17_1_gfblup_variances_all,"T17_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_2_gblup_prediction_all_1_1000=readRDS(file="T17_2_gblup_prediction_all_1_1000.rds") +T17_2_gblup_prediction_all_1001_2000=readRDS(file="T17_2_gblup_prediction_all_1001_2000.rds") +T17_2_gblup_prediction_all_2001_3000=readRDS(file="T17_2_gblup_prediction_all_2001_3000.rds") +T17_2_gblup_prediction_all_3001_4000=readRDS(file="T17_2_gblup_prediction_all_3001_4000.rds") +T17_2_gblup_prediction_all_4001_5000=readRDS(file="T17_2_gblup_prediction_all_4001_5000.rds") +T17_2_gblup_prediction_all_5001_6000=readRDS(file="T17_2_gblup_prediction_all_5001_6000.rds") +T17_2_gblup_prediction_all_6001_7000=readRDS(file="T17_2_gblup_prediction_all_6001_7000.rds") +T17_2_gblup_prediction_all_7001_8000=readRDS(file="T17_2_gblup_prediction_all_7001_8000.rds") +T17_2_gblup_prediction_all_8001_9000=readRDS(file="T17_2_gblup_prediction_all_8001_9000.rds") +T17_2_gblup_prediction_all_9001_10000=readRDS(file="T17_2_gblup_prediction_all_9001_10000.rds") +T17_2_gblup_prediction_all_10001_11000=readRDS(file="T17_2_gblup_prediction_all_10001_11000.rds") +T17_2_gblup_prediction_all_11001_12419=readRDS(file="T17_2_gblup_prediction_all_11001_12419.rds") +T17_2_gblup_prediction_all=c(T17_2_gblup_prediction_all_1_1000,T17_2_gblup_prediction_all_1001_2000,T17_2_gblup_prediction_all_2001_3000,T17_2_gblup_prediction_all_3001_4000,T17_2_gblup_prediction_all_4001_5000,T17_2_gblup_prediction_all_5001_6000,T17_2_gblup_prediction_all_6001_7000,T17_2_gblup_prediction_all_7001_8000,T17_2_gblup_prediction_all_8001_9000,T17_2_gblup_prediction_all_9001_10000,T17_2_gblup_prediction_all_10001_11000,T17_2_gblup_prediction_all_11001_12419) + +T17_2_gblup_variances_all_1_1000=readRDS(file="T17_2_gblup_variances_all_1_1000.rds") +T17_2_gblup_variances_all_1001_2000=readRDS(file="T17_2_gblup_variances_all_1001_2000.rds") +T17_2_gblup_variances_all_2001_3000=readRDS(file="T17_2_gblup_variances_all_2001_3000.rds") +T17_2_gblup_variances_all_3001_4000=readRDS(file="T17_2_gblup_variances_all_3001_4000.rds") +T17_2_gblup_variances_all_4001_5000=readRDS(file="T17_2_gblup_variances_all_4001_5000.rds") +T17_2_gblup_variances_all_5001_6000=readRDS(file="T17_2_gblup_variances_all_5001_6000.rds") +T17_2_gblup_variances_all_6001_7000=readRDS(file="T17_2_gblup_variances_all_6001_7000.rds") +T17_2_gblup_variances_all_7001_8000=readRDS(file="T17_2_gblup_variances_all_7001_8000.rds") +T17_2_gblup_variances_all_8001_9000=readRDS(file="T17_2_gblup_variances_all_8001_9000.rds") +T17_2_gblup_variances_all_9001_10000=readRDS(file="T17_2_gblup_variances_all_9001_10000.rds") +T17_2_gblup_variances_all_10001_11000=readRDS(file="T17_2_gblup_variances_all_10001_11000.rds") +T17_2_gblup_variances_all_11001_12419=readRDS(file="T17_2_gblup_variances_all_11001_12419.rds") +T17_2_gblup_variances_all=c(T17_2_gblup_variances_all_1_1000,T17_2_gblup_variances_all_1001_2000,T17_2_gblup_variances_all_2001_3000,T17_2_gblup_variances_all_3001_4000,T17_2_gblup_variances_all_4001_5000,T17_2_gblup_variances_all_5001_6000,T17_2_gblup_variances_all_6001_7000,T17_2_gblup_variances_all_7001_8000,T17_2_gblup_variances_all_8001_9000,T17_2_gblup_variances_all_9001_10000,T17_2_gblup_variances_all_10001_11000,T17_2_gblup_variances_all_11001_12419) + +saveRDS(T17_2_gblup_prediction_all,"T17_2_gblup_prediction_all.rds") +saveRDS(T17_2_gblup_variances_all,"T17_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_2_gfblup_prediction_all_1_1000=readRDS(file="T17_2_gfblup_prediction_all_1_1000.rds") +T17_2_gfblup_prediction_all_1001_2000=readRDS(file="T17_2_gfblup_prediction_all_1001_2000.rds") +T17_2_gfblup_prediction_all_2001_3000=readRDS(file="T17_2_gfblup_prediction_all_2001_3000.rds") +T17_2_gfblup_prediction_all_3001_4000=readRDS(file="T17_2_gfblup_prediction_all_3001_4000.rds") +T17_2_gfblup_prediction_all_4001_5000=readRDS(file="T17_2_gfblup_prediction_all_4001_5000.rds") +T17_2_gfblup_prediction_all_5001_6000=readRDS(file="T17_2_gfblup_prediction_all_5001_6000.rds") +T17_2_gfblup_prediction_all_6001_7000=readRDS(file="T17_2_gfblup_prediction_all_6001_7000.rds") +T17_2_gfblup_prediction_all_7001_8000=readRDS(file="T17_2_gfblup_prediction_all_7001_8000.rds") +T17_2_gfblup_prediction_all_8001_9000=readRDS(file="T17_2_gfblup_prediction_all_8001_9000.rds") +T17_2_gfblup_prediction_all_9001_10000=readRDS(file="T17_2_gfblup_prediction_all_9001_10000.rds") +T17_2_gfblup_prediction_all_10001_11000=readRDS(file="T17_2_gfblup_prediction_all_10001_11000.rds") +T17_2_gfblup_prediction_all_11001_12419=readRDS(file="T17_2_gfblup_prediction_all_11001_12419.rds") + +T17_2_gfblup_variances_all_1_1000=readRDS(file="T17_2_gfblup_variances_all_1_1000.rds") +T17_2_gfblup_variances_all_1001_2000=readRDS(file="T17_2_gfblup_variances_all_1001_2000.rds") +T17_2_gfblup_variances_all_2001_3000=readRDS(file="T17_2_gfblup_variances_all_2001_3000.rds") +T17_2_gfblup_variances_all_3001_4000=readRDS(file="T17_2_gfblup_variances_all_3001_4000.rds") +T17_2_gfblup_variances_all_4001_5000=readRDS(file="T17_2_gfblup_variances_all_4001_5000.rds") +T17_2_gfblup_variances_all_5001_6000=readRDS(file="T17_2_gfblup_variances_all_5001_6000.rds") +T17_2_gfblup_variances_all_6001_7000=readRDS(file="T17_2_gfblup_variances_all_6001_7000.rds") +T17_2_gfblup_variances_all_7001_8000=readRDS(file="T17_2_gfblup_variances_all_7001_8000.rds") +T17_2_gfblup_variances_all_8001_9000=readRDS(file="T17_2_gfblup_variances_all_8001_9000.rds") +T17_2_gfblup_variances_all_9001_10000=readRDS(file="T17_2_gfblup_variances_all_9001_10000.rds") +T17_2_gfblup_variances_all_10001_11000=readRDS(file="T17_2_gfblup_variances_all_10001_11000.rds") +T17_2_gfblup_variances_all_11001_12419=readRDS(file="T17_2_gfblup_variances_all_11001_12419.rds") + +cycles=length(T17_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T17_2_gfblup_variances_all=rep(list(list()),cycles) +T17_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_1_1000[[r]]) + T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_1001_2000[[r]]) + T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_2001_3000[[r]]) + T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_3001_4000[[r]]) + T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_4001_5000[[r]]) + T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_5001_6000[[r]]) + T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_6001_7000[[r]]) + T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_7001_8000[[r]]) + T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_8001_9000[[r]]) + T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_9001_10000[[r]]) + T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_10001_11000[[r]]) + T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_11001_12419[[r]]) + + T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_1_1000[[r]]) + T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_1001_2000[[r]]) + T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_2001_3000[[r]]) + T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_3001_4000[[r]]) + T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_4001_5000[[r]]) + T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_5001_6000[[r]]) + T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_6001_7000[[r]]) + T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_7001_8000[[r]]) + T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_8001_9000[[r]]) + T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_9001_10000[[r]]) + T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_10001_11000[[r]]) + T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T17_2_gfblup_prediction_all,"T17_2_gfblup_prediction_all.rds") +saveRDS(T17_2_gfblup_variances_all,"T17_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_3_gblup_prediction_all_1_1000=readRDS(file="T17_3_gblup_prediction_all_1_1000.rds") +T17_3_gblup_prediction_all_1001_2000=readRDS(file="T17_3_gblup_prediction_all_1001_2000.rds") +T17_3_gblup_prediction_all_2001_3000=readRDS(file="T17_3_gblup_prediction_all_2001_3000.rds") +T17_3_gblup_prediction_all_3001_4000=readRDS(file="T17_3_gblup_prediction_all_3001_4000.rds") +T17_3_gblup_prediction_all_4001_5000=readRDS(file="T17_3_gblup_prediction_all_4001_5000.rds") +T17_3_gblup_prediction_all_5001_6000=readRDS(file="T17_3_gblup_prediction_all_5001_6000.rds") +T17_3_gblup_prediction_all_6001_7000=readRDS(file="T17_3_gblup_prediction_all_6001_7000.rds") +T17_3_gblup_prediction_all_7001_8000=readRDS(file="T17_3_gblup_prediction_all_7001_8000.rds") +T17_3_gblup_prediction_all_8001_9000=readRDS(file="T17_3_gblup_prediction_all_8001_9000.rds") +T17_3_gblup_prediction_all_9001_10000=readRDS(file="T17_3_gblup_prediction_all_9001_10000.rds") +T17_3_gblup_prediction_all_10001_11000=readRDS(file="T17_3_gblup_prediction_all_10001_11000.rds") +T17_3_gblup_prediction_all_11001_12419=readRDS(file="T17_3_gblup_prediction_all_11001_12419.rds") +T17_3_gblup_prediction_all=c(T17_3_gblup_prediction_all_1_1000,T17_3_gblup_prediction_all_1001_2000,T17_3_gblup_prediction_all_2001_3000,T17_3_gblup_prediction_all_3001_4000,T17_3_gblup_prediction_all_4001_5000,T17_3_gblup_prediction_all_5001_6000,T17_3_gblup_prediction_all_6001_7000,T17_3_gblup_prediction_all_7001_8000,T17_3_gblup_prediction_all_8001_9000,T17_3_gblup_prediction_all_9001_10000,T17_3_gblup_prediction_all_10001_11000,T17_3_gblup_prediction_all_11001_12419) + +T17_3_gblup_variances_all_1_1000=readRDS(file="T17_3_gblup_variances_all_1_1000.rds") +T17_3_gblup_variances_all_1001_2000=readRDS(file="T17_3_gblup_variances_all_1001_2000.rds") +T17_3_gblup_variances_all_2001_3000=readRDS(file="T17_3_gblup_variances_all_2001_3000.rds") +T17_3_gblup_variances_all_3001_4000=readRDS(file="T17_3_gblup_variances_all_3001_4000.rds") +T17_3_gblup_variances_all_4001_5000=readRDS(file="T17_3_gblup_variances_all_4001_5000.rds") +T17_3_gblup_variances_all_5001_6000=readRDS(file="T17_3_gblup_variances_all_5001_6000.rds") +T17_3_gblup_variances_all_6001_7000=readRDS(file="T17_3_gblup_variances_all_6001_7000.rds") +T17_3_gblup_variances_all_7001_8000=readRDS(file="T17_3_gblup_variances_all_7001_8000.rds") +T17_3_gblup_variances_all_8001_9000=readRDS(file="T17_3_gblup_variances_all_8001_9000.rds") +T17_3_gblup_variances_all_9001_10000=readRDS(file="T17_3_gblup_variances_all_9001_10000.rds") +T17_3_gblup_variances_all_10001_11000=readRDS(file="T17_3_gblup_variances_all_10001_11000.rds") +T17_3_gblup_variances_all_11001_12419=readRDS(file="T17_3_gblup_variances_all_11001_12419.rds") +T17_3_gblup_variances_all=c(T17_3_gblup_variances_all_1_1000,T17_3_gblup_variances_all_1001_2000,T17_3_gblup_variances_all_2001_3000,T17_3_gblup_variances_all_3001_4000,T17_3_gblup_variances_all_4001_5000,T17_3_gblup_variances_all_5001_6000,T17_3_gblup_variances_all_6001_7000,T17_3_gblup_variances_all_7001_8000,T17_3_gblup_variances_all_8001_9000,T17_3_gblup_variances_all_9001_10000,T17_3_gblup_variances_all_10001_11000,T17_3_gblup_variances_all_11001_12419) + +saveRDS(T17_3_gblup_prediction_all,"T17_3_gblup_prediction_all.rds") +saveRDS(T17_3_gblup_variances_all,"T17_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_3_gfblup_prediction_all_1_1000=readRDS(file="T17_3_gfblup_prediction_all_1_1000.rds") +T17_3_gfblup_prediction_all_1001_2000=readRDS(file="T17_3_gfblup_prediction_all_1001_2000.rds") +T17_3_gfblup_prediction_all_2001_3000=readRDS(file="T17_3_gfblup_prediction_all_2001_3000.rds") +T17_3_gfblup_prediction_all_3001_4000=readRDS(file="T17_3_gfblup_prediction_all_3001_4000.rds") +T17_3_gfblup_prediction_all_4001_5000=readRDS(file="T17_3_gfblup_prediction_all_4001_5000.rds") +T17_3_gfblup_prediction_all_5001_6000=readRDS(file="T17_3_gfblup_prediction_all_5001_6000.rds") +T17_3_gfblup_prediction_all_6001_7000=readRDS(file="T17_3_gfblup_prediction_all_6001_7000.rds") +T17_3_gfblup_prediction_all_7001_8000=readRDS(file="T17_3_gfblup_prediction_all_7001_8000.rds") +T17_3_gfblup_prediction_all_8001_9000=readRDS(file="T17_3_gfblup_prediction_all_8001_9000.rds") +T17_3_gfblup_prediction_all_9001_10000=readRDS(file="T17_3_gfblup_prediction_all_9001_10000.rds") +T17_3_gfblup_prediction_all_10001_11000=readRDS(file="T17_3_gfblup_prediction_all_10001_11000.rds") +T17_3_gfblup_prediction_all_11001_12419=readRDS(file="T17_3_gfblup_prediction_all_11001_12419.rds") + +T17_3_gfblup_variances_all_1_1000=readRDS(file="T17_3_gfblup_variances_all_1_1000.rds") +T17_3_gfblup_variances_all_1001_2000=readRDS(file="T17_3_gfblup_variances_all_1001_2000.rds") +T17_3_gfblup_variances_all_2001_3000=readRDS(file="T17_3_gfblup_variances_all_2001_3000.rds") +T17_3_gfblup_variances_all_3001_4000=readRDS(file="T17_3_gfblup_variances_all_3001_4000.rds") +T17_3_gfblup_variances_all_4001_5000=readRDS(file="T17_3_gfblup_variances_all_4001_5000.rds") +T17_3_gfblup_variances_all_5001_6000=readRDS(file="T17_3_gfblup_variances_all_5001_6000.rds") +T17_3_gfblup_variances_all_6001_7000=readRDS(file="T17_3_gfblup_variances_all_6001_7000.rds") +T17_3_gfblup_variances_all_7001_8000=readRDS(file="T17_3_gfblup_variances_all_7001_8000.rds") +T17_3_gfblup_variances_all_8001_9000=readRDS(file="T17_3_gfblup_variances_all_8001_9000.rds") +T17_3_gfblup_variances_all_9001_10000=readRDS(file="T17_3_gfblup_variances_all_9001_10000.rds") +T17_3_gfblup_variances_all_10001_11000=readRDS(file="T17_3_gfblup_variances_all_10001_11000.rds") +T17_3_gfblup_variances_all_11001_12419=readRDS(file="T17_3_gfblup_variances_all_11001_12419.rds") + +cycles=length(T17_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T17_3_gfblup_variances_all=rep(list(list()),cycles) +T17_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_1_1000[[r]]) + T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_1001_2000[[r]]) + T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_2001_3000[[r]]) + T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_3001_4000[[r]]) + T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_4001_5000[[r]]) + T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_5001_6000[[r]]) + T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_6001_7000[[r]]) + T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_7001_8000[[r]]) + T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_8001_9000[[r]]) + T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_9001_10000[[r]]) + T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_10001_11000[[r]]) + T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_11001_12419[[r]]) + + T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_1_1000[[r]]) + T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_1001_2000[[r]]) + T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_2001_3000[[r]]) + T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_3001_4000[[r]]) + T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_4001_5000[[r]]) + T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_5001_6000[[r]]) + T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_6001_7000[[r]]) + T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_7001_8000[[r]]) + T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_8001_9000[[r]]) + T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_9001_10000[[r]]) + T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_10001_11000[[r]]) + T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T17_3_gfblup_prediction_all,"T17_3_gfblup_prediction_all.rds") +saveRDS(T17_3_gfblup_variances_all,"T17_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_4_gblup_prediction_all_1_1000=readRDS(file="T17_4_gblup_prediction_all_1_1000.rds") +T17_4_gblup_prediction_all_1001_2000=readRDS(file="T17_4_gblup_prediction_all_1001_2000.rds") +T17_4_gblup_prediction_all_2001_3000=readRDS(file="T17_4_gblup_prediction_all_2001_3000.rds") +T17_4_gblup_prediction_all_3001_4000=readRDS(file="T17_4_gblup_prediction_all_3001_4000.rds") +T17_4_gblup_prediction_all_4001_5000=readRDS(file="T17_4_gblup_prediction_all_4001_5000.rds") +T17_4_gblup_prediction_all_5001_6000=readRDS(file="T17_4_gblup_prediction_all_5001_6000.rds") +T17_4_gblup_prediction_all_6001_7000=readRDS(file="T17_4_gblup_prediction_all_6001_7000.rds") +T17_4_gblup_prediction_all_7001_8000=readRDS(file="T17_4_gblup_prediction_all_7001_8000.rds") +T17_4_gblup_prediction_all_8001_9000=readRDS(file="T17_4_gblup_prediction_all_8001_9000.rds") +T17_4_gblup_prediction_all_9001_10000=readRDS(file="T17_4_gblup_prediction_all_9001_10000.rds") +T17_4_gblup_prediction_all_10001_11000=readRDS(file="T17_4_gblup_prediction_all_10001_11000.rds") +T17_4_gblup_prediction_all_11001_12419=readRDS(file="T17_4_gblup_prediction_all_11001_12419.rds") +T17_4_gblup_prediction_all=c(T17_4_gblup_prediction_all_1_1000,T17_4_gblup_prediction_all_1001_2000,T17_4_gblup_prediction_all_2001_3000,T17_4_gblup_prediction_all_3001_4000,T17_4_gblup_prediction_all_4001_5000,T17_4_gblup_prediction_all_5001_6000,T17_4_gblup_prediction_all_6001_7000,T17_4_gblup_prediction_all_7001_8000,T17_4_gblup_prediction_all_8001_9000,T17_4_gblup_prediction_all_9001_10000,T17_4_gblup_prediction_all_10001_11000,T17_4_gblup_prediction_all_11001_12419) + +T17_4_gblup_variances_all_1_1000=readRDS(file="T17_4_gblup_variances_all_1_1000.rds") +T17_4_gblup_variances_all_1001_2000=readRDS(file="T17_4_gblup_variances_all_1001_2000.rds") +T17_4_gblup_variances_all_2001_3000=readRDS(file="T17_4_gblup_variances_all_2001_3000.rds") +T17_4_gblup_variances_all_3001_4000=readRDS(file="T17_4_gblup_variances_all_3001_4000.rds") +T17_4_gblup_variances_all_4001_5000=readRDS(file="T17_4_gblup_variances_all_4001_5000.rds") +T17_4_gblup_variances_all_5001_6000=readRDS(file="T17_4_gblup_variances_all_5001_6000.rds") +T17_4_gblup_variances_all_6001_7000=readRDS(file="T17_4_gblup_variances_all_6001_7000.rds") +T17_4_gblup_variances_all_7001_8000=readRDS(file="T17_4_gblup_variances_all_7001_8000.rds") +T17_4_gblup_variances_all_8001_9000=readRDS(file="T17_4_gblup_variances_all_8001_9000.rds") +T17_4_gblup_variances_all_9001_10000=readRDS(file="T17_4_gblup_variances_all_9001_10000.rds") +T17_4_gblup_variances_all_10001_11000=readRDS(file="T17_4_gblup_variances_all_10001_11000.rds") +T17_4_gblup_variances_all_11001_12419=readRDS(file="T17_4_gblup_variances_all_11001_12419.rds") +T17_4_gblup_variances_all=c(T17_4_gblup_variances_all_1_1000,T17_4_gblup_variances_all_1001_2000,T17_4_gblup_variances_all_2001_3000,T17_4_gblup_variances_all_3001_4000,T17_4_gblup_variances_all_4001_5000,T17_4_gblup_variances_all_5001_6000,T17_4_gblup_variances_all_6001_7000,T17_4_gblup_variances_all_7001_8000,T17_4_gblup_variances_all_8001_9000,T17_4_gblup_variances_all_9001_10000,T17_4_gblup_variances_all_10001_11000,T17_4_gblup_variances_all_11001_12419) + +saveRDS(T17_4_gblup_prediction_all,"T17_4_gblup_prediction_all.rds") +saveRDS(T17_4_gblup_variances_all,"T17_4_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_4_gfblup_prediction_all_1_1000=readRDS(file="T17_4_gfblup_prediction_all_1_1000.rds") +T17_4_gfblup_prediction_all_1001_2000=readRDS(file="T17_4_gfblup_prediction_all_1001_2000.rds") +T17_4_gfblup_prediction_all_2001_3000=readRDS(file="T17_4_gfblup_prediction_all_2001_3000.rds") +T17_4_gfblup_prediction_all_3001_4000=readRDS(file="T17_4_gfblup_prediction_all_3001_4000.rds") +T17_4_gfblup_prediction_all_4001_5000=readRDS(file="T17_4_gfblup_prediction_all_4001_5000.rds") +T17_4_gfblup_prediction_all_5001_6000=readRDS(file="T17_4_gfblup_prediction_all_5001_6000.rds") +T17_4_gfblup_prediction_all_6001_7000=readRDS(file="T17_4_gfblup_prediction_all_6001_7000.rds") +T17_4_gfblup_prediction_all_7001_8000=readRDS(file="T17_4_gfblup_prediction_all_7001_8000.rds") +T17_4_gfblup_prediction_all_8001_9000=readRDS(file="T17_4_gfblup_prediction_all_8001_9000.rds") +T17_4_gfblup_prediction_all_9001_10000=readRDS(file="T17_4_gfblup_prediction_all_9001_10000.rds") +T17_4_gfblup_prediction_all_10001_11000=readRDS(file="T17_4_gfblup_prediction_all_10001_11000.rds") +T17_4_gfblup_prediction_all_11001_12419=readRDS(file="T17_4_gfblup_prediction_all_11001_12419.rds") + +T17_4_gfblup_variances_all_1_1000=readRDS(file="T17_4_gfblup_variances_all_1_1000.rds") +T17_4_gfblup_variances_all_1001_2000=readRDS(file="T17_4_gfblup_variances_all_1001_2000.rds") +T17_4_gfblup_variances_all_2001_3000=readRDS(file="T17_4_gfblup_variances_all_2001_3000.rds") +T17_4_gfblup_variances_all_3001_4000=readRDS(file="T17_4_gfblup_variances_all_3001_4000.rds") +T17_4_gfblup_variances_all_4001_5000=readRDS(file="T17_4_gfblup_variances_all_4001_5000.rds") +T17_4_gfblup_variances_all_5001_6000=readRDS(file="T17_4_gfblup_variances_all_5001_6000.rds") +T17_4_gfblup_variances_all_6001_7000=readRDS(file="T17_4_gfblup_variances_all_6001_7000.rds") +T17_4_gfblup_variances_all_7001_8000=readRDS(file="T17_4_gfblup_variances_all_7001_8000.rds") +T17_4_gfblup_variances_all_8001_9000=readRDS(file="T17_4_gfblup_variances_all_8001_9000.rds") +T17_4_gfblup_variances_all_9001_10000=readRDS(file="T17_4_gfblup_variances_all_9001_10000.rds") +T17_4_gfblup_variances_all_10001_11000=readRDS(file="T17_4_gfblup_variances_all_10001_11000.rds") +T17_4_gfblup_variances_all_11001_12419=readRDS(file="T17_4_gfblup_variances_all_11001_12419.rds") + +cycles=length(T17_4_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T17_4_gfblup_variances_all=rep(list(list()),cycles) +T17_4_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_1_1000[[r]]) + T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_1001_2000[[r]]) + T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_2001_3000[[r]]) + T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_3001_4000[[r]]) + T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_4001_5000[[r]]) + T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_5001_6000[[r]]) + T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_6001_7000[[r]]) + T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_7001_8000[[r]]) + T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_8001_9000[[r]]) + T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_9001_10000[[r]]) + T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_10001_11000[[r]]) + T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_11001_12419[[r]]) + + T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_1_1000[[r]]) + T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_1001_2000[[r]]) + T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_2001_3000[[r]]) + T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_3001_4000[[r]]) + T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_4001_5000[[r]]) + T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_5001_6000[[r]]) + T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_6001_7000[[r]]) + T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_7001_8000[[r]]) + T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_8001_9000[[r]]) + T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_9001_10000[[r]]) + T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_10001_11000[[r]]) + T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T17_4_gfblup_prediction_all,"T17_4_gfblup_prediction_all.rds") +saveRDS(T17_4_gfblup_variances_all,"T17_4_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_5_gblup_prediction_all_1_1000=readRDS(file="T17_5_gblup_prediction_all_1_1000.rds") +T17_5_gblup_prediction_all_1001_2000=readRDS(file="T17_5_gblup_prediction_all_1001_2000.rds") +T17_5_gblup_prediction_all_2001_3000=readRDS(file="T17_5_gblup_prediction_all_2001_3000.rds") +T17_5_gblup_prediction_all_3001_4000=readRDS(file="T17_5_gblup_prediction_all_3001_4000.rds") +T17_5_gblup_prediction_all_4001_5000=readRDS(file="T17_5_gblup_prediction_all_4001_5000.rds") +T17_5_gblup_prediction_all_5001_6000=readRDS(file="T17_5_gblup_prediction_all_5001_6000.rds") +T17_5_gblup_prediction_all_6001_7000=readRDS(file="T17_5_gblup_prediction_all_6001_7000.rds") +T17_5_gblup_prediction_all_7001_8000=readRDS(file="T17_5_gblup_prediction_all_7001_8000.rds") +T17_5_gblup_prediction_all_8001_9000=readRDS(file="T17_5_gblup_prediction_all_8001_9000.rds") +T17_5_gblup_prediction_all_9001_10000=readRDS(file="T17_5_gblup_prediction_all_9001_10000.rds") +T17_5_gblup_prediction_all_10001_11000=readRDS(file="T17_5_gblup_prediction_all_10001_11000.rds") +T17_5_gblup_prediction_all_11001_12419=readRDS(file="T17_5_gblup_prediction_all_11001_12419.rds") +T17_5_gblup_prediction_all=c(T17_5_gblup_prediction_all_1_1000,T17_5_gblup_prediction_all_1001_2000,T17_5_gblup_prediction_all_2001_3000,T17_5_gblup_prediction_all_3001_4000,T17_5_gblup_prediction_all_4001_5000,T17_5_gblup_prediction_all_5001_6000,T17_5_gblup_prediction_all_6001_7000,T17_5_gblup_prediction_all_7001_8000,T17_5_gblup_prediction_all_8001_9000,T17_5_gblup_prediction_all_9001_10000,T17_5_gblup_prediction_all_10001_11000,T17_5_gblup_prediction_all_11001_12419) + +T17_5_gblup_variances_all_1_1000=readRDS(file="T17_5_gblup_variances_all_1_1000.rds") +T17_5_gblup_variances_all_1001_2000=readRDS(file="T17_5_gblup_variances_all_1001_2000.rds") +T17_5_gblup_variances_all_2001_3000=readRDS(file="T17_5_gblup_variances_all_2001_3000.rds") +T17_5_gblup_variances_all_3001_4000=readRDS(file="T17_5_gblup_variances_all_3001_4000.rds") +T17_5_gblup_variances_all_4001_5000=readRDS(file="T17_5_gblup_variances_all_4001_5000.rds") +T17_5_gblup_variances_all_5001_6000=readRDS(file="T17_5_gblup_variances_all_5001_6000.rds") +T17_5_gblup_variances_all_6001_7000=readRDS(file="T17_5_gblup_variances_all_6001_7000.rds") +T17_5_gblup_variances_all_7001_8000=readRDS(file="T17_5_gblup_variances_all_7001_8000.rds") +T17_5_gblup_variances_all_8001_9000=readRDS(file="T17_5_gblup_variances_all_8001_9000.rds") +T17_5_gblup_variances_all_9001_10000=readRDS(file="T17_5_gblup_variances_all_9001_10000.rds") +T17_5_gblup_variances_all_10001_11000=readRDS(file="T17_5_gblup_variances_all_10001_11000.rds") +T17_5_gblup_variances_all_11001_12419=readRDS(file="T17_5_gblup_variances_all_11001_12419.rds") +T17_5_gblup_variances_all=c(T17_5_gblup_variances_all_1_1000,T17_5_gblup_variances_all_1001_2000,T17_5_gblup_variances_all_2001_3000,T17_5_gblup_variances_all_3001_4000,T17_5_gblup_variances_all_4001_5000,T17_5_gblup_variances_all_5001_6000,T17_5_gblup_variances_all_6001_7000,T17_5_gblup_variances_all_7001_8000,T17_5_gblup_variances_all_8001_9000,T17_5_gblup_variances_all_9001_10000,T17_5_gblup_variances_all_10001_11000,T17_5_gblup_variances_all_11001_12419) + +saveRDS(T17_5_gblup_prediction_all,"T17_5_gblup_prediction_all.rds") +saveRDS(T17_5_gblup_variances_all,"T17_5_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_5_gfblup_prediction_all_1_1000=readRDS(file="T17_5_gfblup_prediction_all_1_1000.rds") +T17_5_gfblup_prediction_all_1001_2000=readRDS(file="T17_5_gfblup_prediction_all_1001_2000.rds") +T17_5_gfblup_prediction_all_2001_3000=readRDS(file="T17_5_gfblup_prediction_all_2001_3000.rds") +T17_5_gfblup_prediction_all_3001_4000=readRDS(file="T17_5_gfblup_prediction_all_3001_4000.rds") +T17_5_gfblup_prediction_all_4001_5000=readRDS(file="T17_5_gfblup_prediction_all_4001_5000.rds") +T17_5_gfblup_prediction_all_5001_6000=readRDS(file="T17_5_gfblup_prediction_all_5001_6000.rds") +T17_5_gfblup_prediction_all_6001_7000=readRDS(file="T17_5_gfblup_prediction_all_6001_7000.rds") +T17_5_gfblup_prediction_all_7001_8000=readRDS(file="T17_5_gfblup_prediction_all_7001_8000.rds") +T17_5_gfblup_prediction_all_8001_9000=readRDS(file="T17_5_gfblup_prediction_all_8001_9000.rds") +T17_5_gfblup_prediction_all_9001_10000=readRDS(file="T17_5_gfblup_prediction_all_9001_10000.rds") +T17_5_gfblup_prediction_all_10001_11000=readRDS(file="T17_5_gfblup_prediction_all_10001_11000.rds") +T17_5_gfblup_prediction_all_11001_12419=readRDS(file="T17_5_gfblup_prediction_all_11001_12419.rds") + +T17_5_gfblup_variances_all_1_1000=readRDS(file="T17_5_gfblup_variances_all_1_1000.rds") +T17_5_gfblup_variances_all_1001_2000=readRDS(file="T17_5_gfblup_variances_all_1001_2000.rds") +T17_5_gfblup_variances_all_2001_3000=readRDS(file="T17_5_gfblup_variances_all_2001_3000.rds") +T17_5_gfblup_variances_all_3001_4000=readRDS(file="T17_5_gfblup_variances_all_3001_4000.rds") +T17_5_gfblup_variances_all_4001_5000=readRDS(file="T17_5_gfblup_variances_all_4001_5000.rds") +T17_5_gfblup_variances_all_5001_6000=readRDS(file="T17_5_gfblup_variances_all_5001_6000.rds") +T17_5_gfblup_variances_all_6001_7000=readRDS(file="T17_5_gfblup_variances_all_6001_7000.rds") +T17_5_gfblup_variances_all_7001_8000=readRDS(file="T17_5_gfblup_variances_all_7001_8000.rds") +T17_5_gfblup_variances_all_8001_9000=readRDS(file="T17_5_gfblup_variances_all_8001_9000.rds") +T17_5_gfblup_variances_all_9001_10000=readRDS(file="T17_5_gfblup_variances_all_9001_10000.rds") +T17_5_gfblup_variances_all_10001_11000=readRDS(file="T17_5_gfblup_variances_all_10001_11000.rds") +T17_5_gfblup_variances_all_11001_12419=readRDS(file="T17_5_gfblup_variances_all_11001_12419.rds") + +cycles=length(T17_5_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T17_5_gfblup_variances_all=rep(list(list()),cycles) +T17_5_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_1_1000[[r]]) + T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_1001_2000[[r]]) + T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_2001_3000[[r]]) + T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_3001_4000[[r]]) + T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_4001_5000[[r]]) + T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_5001_6000[[r]]) + T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_6001_7000[[r]]) + T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_7001_8000[[r]]) + T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_8001_9000[[r]]) + T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_9001_10000[[r]]) + T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_10001_11000[[r]]) + T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_11001_12419[[r]]) + + T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_1_1000[[r]]) + T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_1001_2000[[r]]) + T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_2001_3000[[r]]) + T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_3001_4000[[r]]) + T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_4001_5000[[r]]) + T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_5001_6000[[r]]) + T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_6001_7000[[r]]) + T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_7001_8000[[r]]) + T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_8001_9000[[r]]) + T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_9001_10000[[r]]) + T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_10001_11000[[r]]) + T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T17_5_gfblup_prediction_all,"T17_5_gfblup_prediction_all.rds") +saveRDS(T17_5_gfblup_variances_all,"T17_5_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_6_gblup_prediction_all_1_1000=readRDS(file="T17_6_gblup_prediction_all_1_1000.rds") +T17_6_gblup_prediction_all_1001_2000=readRDS(file="T17_6_gblup_prediction_all_1001_2000.rds") +T17_6_gblup_prediction_all_2001_3000=readRDS(file="T17_6_gblup_prediction_all_2001_3000.rds") +T17_6_gblup_prediction_all_3001_4000=readRDS(file="T17_6_gblup_prediction_all_3001_4000.rds") +T17_6_gblup_prediction_all_4001_5000=readRDS(file="T17_6_gblup_prediction_all_4001_5000.rds") +T17_6_gblup_prediction_all_5001_6000=readRDS(file="T17_6_gblup_prediction_all_5001_6000.rds") +T17_6_gblup_prediction_all_6001_7000=readRDS(file="T17_6_gblup_prediction_all_6001_7000.rds") +T17_6_gblup_prediction_all_7001_8000=readRDS(file="T17_6_gblup_prediction_all_7001_8000.rds") +T17_6_gblup_prediction_all_8001_9000=readRDS(file="T17_6_gblup_prediction_all_8001_9000.rds") +T17_6_gblup_prediction_all_9001_10000=readRDS(file="T17_6_gblup_prediction_all_9001_10000.rds") +T17_6_gblup_prediction_all_10001_11000=readRDS(file="T17_6_gblup_prediction_all_10001_11000.rds") +T17_6_gblup_prediction_all_11001_12419=readRDS(file="T17_6_gblup_prediction_all_11001_12419.rds") +T17_6_gblup_prediction_all=c(T17_6_gblup_prediction_all_1_1000,T17_6_gblup_prediction_all_1001_2000,T17_6_gblup_prediction_all_2001_3000,T17_6_gblup_prediction_all_3001_4000,T17_6_gblup_prediction_all_4001_5000,T17_6_gblup_prediction_all_5001_6000,T17_6_gblup_prediction_all_6001_7000,T17_6_gblup_prediction_all_7001_8000,T17_6_gblup_prediction_all_8001_9000,T17_6_gblup_prediction_all_9001_10000,T17_6_gblup_prediction_all_10001_11000,T17_6_gblup_prediction_all_11001_12419) + +T17_6_gblup_variances_all_1_1000=readRDS(file="T17_6_gblup_variances_all_1_1000.rds") +T17_6_gblup_variances_all_1001_2000=readRDS(file="T17_6_gblup_variances_all_1001_2000.rds") +T17_6_gblup_variances_all_2001_3000=readRDS(file="T17_6_gblup_variances_all_2001_3000.rds") +T17_6_gblup_variances_all_3001_4000=readRDS(file="T17_6_gblup_variances_all_3001_4000.rds") +T17_6_gblup_variances_all_4001_5000=readRDS(file="T17_6_gblup_variances_all_4001_5000.rds") +T17_6_gblup_variances_all_5001_6000=readRDS(file="T17_6_gblup_variances_all_5001_6000.rds") +T17_6_gblup_variances_all_6001_7000=readRDS(file="T17_6_gblup_variances_all_6001_7000.rds") +T17_6_gblup_variances_all_7001_8000=readRDS(file="T17_6_gblup_variances_all_7001_8000.rds") +T17_6_gblup_variances_all_8001_9000=readRDS(file="T17_6_gblup_variances_all_8001_9000.rds") +T17_6_gblup_variances_all_9001_10000=readRDS(file="T17_6_gblup_variances_all_9001_10000.rds") +T17_6_gblup_variances_all_10001_11000=readRDS(file="T17_6_gblup_variances_all_10001_11000.rds") +T17_6_gblup_variances_all_11001_12419=readRDS(file="T17_6_gblup_variances_all_11001_12419.rds") +T17_6_gblup_variances_all=c(T17_6_gblup_variances_all_1_1000,T17_6_gblup_variances_all_1001_2000,T17_6_gblup_variances_all_2001_3000,T17_6_gblup_variances_all_3001_4000,T17_6_gblup_variances_all_4001_5000,T17_6_gblup_variances_all_5001_6000,T17_6_gblup_variances_all_6001_7000,T17_6_gblup_variances_all_7001_8000,T17_6_gblup_variances_all_8001_9000,T17_6_gblup_variances_all_9001_10000,T17_6_gblup_variances_all_10001_11000,T17_6_gblup_variances_all_11001_12419) + +saveRDS(T17_6_gblup_prediction_all,"T17_6_gblup_prediction_all.rds") +saveRDS(T17_6_gblup_variances_all,"T17_6_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_6_gfblup_prediction_all_1_1000=readRDS(file="T17_6_gfblup_prediction_all_1_1000.rds") +T17_6_gfblup_prediction_all_1001_2000=readRDS(file="T17_6_gfblup_prediction_all_1001_2000.rds") +T17_6_gfblup_prediction_all_2001_3000=readRDS(file="T17_6_gfblup_prediction_all_2001_3000.rds") +T17_6_gfblup_prediction_all_3001_4000=readRDS(file="T17_6_gfblup_prediction_all_3001_4000.rds") +T17_6_gfblup_prediction_all_4001_5000=readRDS(file="T17_6_gfblup_prediction_all_4001_5000.rds") +T17_6_gfblup_prediction_all_5001_6000=readRDS(file="T17_6_gfblup_prediction_all_5001_6000.rds") +T17_6_gfblup_prediction_all_6001_7000=readRDS(file="T17_6_gfblup_prediction_all_6001_7000.rds") +T17_6_gfblup_prediction_all_7001_8000=readRDS(file="T17_6_gfblup_prediction_all_7001_8000.rds") +T17_6_gfblup_prediction_all_8001_9000=readRDS(file="T17_6_gfblup_prediction_all_8001_9000.rds") +T17_6_gfblup_prediction_all_9001_10000=readRDS(file="T17_6_gfblup_prediction_all_9001_10000.rds") +T17_6_gfblup_prediction_all_10001_11000=readRDS(file="T17_6_gfblup_prediction_all_10001_11000.rds") +T17_6_gfblup_prediction_all_11001_12419=readRDS(file="T17_6_gfblup_prediction_all_11001_12419.rds") + +T17_6_gfblup_variances_all_1_1000=readRDS(file="T17_6_gfblup_variances_all_1_1000.rds") +T17_6_gfblup_variances_all_1001_2000=readRDS(file="T17_6_gfblup_variances_all_1001_2000.rds") +T17_6_gfblup_variances_all_2001_3000=readRDS(file="T17_6_gfblup_variances_all_2001_3000.rds") +T17_6_gfblup_variances_all_3001_4000=readRDS(file="T17_6_gfblup_variances_all_3001_4000.rds") +T17_6_gfblup_variances_all_4001_5000=readRDS(file="T17_6_gfblup_variances_all_4001_5000.rds") +T17_6_gfblup_variances_all_5001_6000=readRDS(file="T17_6_gfblup_variances_all_5001_6000.rds") +T17_6_gfblup_variances_all_6001_7000=readRDS(file="T17_6_gfblup_variances_all_6001_7000.rds") +T17_6_gfblup_variances_all_7001_8000=readRDS(file="T17_6_gfblup_variances_all_7001_8000.rds") +T17_6_gfblup_variances_all_8001_9000=readRDS(file="T17_6_gfblup_variances_all_8001_9000.rds") +T17_6_gfblup_variances_all_9001_10000=readRDS(file="T17_6_gfblup_variances_all_9001_10000.rds") +T17_6_gfblup_variances_all_10001_11000=readRDS(file="T17_6_gfblup_variances_all_10001_11000.rds") +T17_6_gfblup_variances_all_11001_12419=readRDS(file="T17_6_gfblup_variances_all_11001_12419.rds") + +cycles=length(T17_6_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T17_6_gfblup_variances_all=rep(list(list()),cycles) +T17_6_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_1_1000[[r]]) + T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_1001_2000[[r]]) + T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_2001_3000[[r]]) + T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_3001_4000[[r]]) + T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_4001_5000[[r]]) + T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_5001_6000[[r]]) + T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_6001_7000[[r]]) + T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_7001_8000[[r]]) + T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_8001_9000[[r]]) + T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_9001_10000[[r]]) + T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_10001_11000[[r]]) + T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_11001_12419[[r]]) + + T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_1_1000[[r]]) + T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_1001_2000[[r]]) + T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_2001_3000[[r]]) + T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_3001_4000[[r]]) + T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_4001_5000[[r]]) + T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_5001_6000[[r]]) + T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_6001_7000[[r]]) + T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_7001_8000[[r]]) + T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_8001_9000[[r]]) + T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_9001_10000[[r]]) + T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_10001_11000[[r]]) + T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T17_6_gfblup_prediction_all,"T17_6_gfblup_prediction_all.rds") +saveRDS(T17_6_gfblup_variances_all,"T17_6_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_7_gblup_prediction_all_1_1000=readRDS(file="T17_7_gblup_prediction_all_1_1000.rds") +T17_7_gblup_prediction_all_1001_2000=readRDS(file="T17_7_gblup_prediction_all_1001_2000.rds") +T17_7_gblup_prediction_all_2001_3000=readRDS(file="T17_7_gblup_prediction_all_2001_3000.rds") +T17_7_gblup_prediction_all_3001_4000=readRDS(file="T17_7_gblup_prediction_all_3001_4000.rds") +T17_7_gblup_prediction_all_4001_5000=readRDS(file="T17_7_gblup_prediction_all_4001_5000.rds") +T17_7_gblup_prediction_all_5001_6000=readRDS(file="T17_7_gblup_prediction_all_5001_6000.rds") +T17_7_gblup_prediction_all_6001_7000=readRDS(file="T17_7_gblup_prediction_all_6001_7000.rds") +T17_7_gblup_prediction_all_7001_8000=readRDS(file="T17_7_gblup_prediction_all_7001_8000.rds") +T17_7_gblup_prediction_all_8001_9000=readRDS(file="T17_7_gblup_prediction_all_8001_9000.rds") +T17_7_gblup_prediction_all_9001_10000=readRDS(file="T17_7_gblup_prediction_all_9001_10000.rds") +T17_7_gblup_prediction_all_10001_11000=readRDS(file="T17_7_gblup_prediction_all_10001_11000.rds") +T17_7_gblup_prediction_all_11001_12419=readRDS(file="T17_7_gblup_prediction_all_11001_12419.rds") +T17_7_gblup_prediction_all=c(T17_7_gblup_prediction_all_1_1000,T17_7_gblup_prediction_all_1001_2000,T17_7_gblup_prediction_all_2001_3000,T17_7_gblup_prediction_all_3001_4000,T17_7_gblup_prediction_all_4001_5000,T17_7_gblup_prediction_all_5001_6000,T17_7_gblup_prediction_all_6001_7000,T17_7_gblup_prediction_all_7001_8000,T17_7_gblup_prediction_all_8001_9000,T17_7_gblup_prediction_all_9001_10000,T17_7_gblup_prediction_all_10001_11000,T17_7_gblup_prediction_all_11001_12419) + +T17_7_gblup_variances_all_1_1000=readRDS(file="T17_7_gblup_variances_all_1_1000.rds") +T17_7_gblup_variances_all_1001_2000=readRDS(file="T17_7_gblup_variances_all_1001_2000.rds") +T17_7_gblup_variances_all_2001_3000=readRDS(file="T17_7_gblup_variances_all_2001_3000.rds") +T17_7_gblup_variances_all_3001_4000=readRDS(file="T17_7_gblup_variances_all_3001_4000.rds") +T17_7_gblup_variances_all_4001_5000=readRDS(file="T17_7_gblup_variances_all_4001_5000.rds") +T17_7_gblup_variances_all_5001_6000=readRDS(file="T17_7_gblup_variances_all_5001_6000.rds") +T17_7_gblup_variances_all_6001_7000=readRDS(file="T17_7_gblup_variances_all_6001_7000.rds") +T17_7_gblup_variances_all_7001_8000=readRDS(file="T17_7_gblup_variances_all_7001_8000.rds") +T17_7_gblup_variances_all_8001_9000=readRDS(file="T17_7_gblup_variances_all_8001_9000.rds") +T17_7_gblup_variances_all_9001_10000=readRDS(file="T17_7_gblup_variances_all_9001_10000.rds") +T17_7_gblup_variances_all_10001_11000=readRDS(file="T17_7_gblup_variances_all_10001_11000.rds") +T17_7_gblup_variances_all_11001_12419=readRDS(file="T17_7_gblup_variances_all_11001_12419.rds") +T17_7_gblup_variances_all=c(T17_7_gblup_variances_all_1_1000,T17_7_gblup_variances_all_1001_2000,T17_7_gblup_variances_all_2001_3000,T17_7_gblup_variances_all_3001_4000,T17_7_gblup_variances_all_4001_5000,T17_7_gblup_variances_all_5001_6000,T17_7_gblup_variances_all_6001_7000,T17_7_gblup_variances_all_7001_8000,T17_7_gblup_variances_all_8001_9000,T17_7_gblup_variances_all_9001_10000,T17_7_gblup_variances_all_10001_11000,T17_7_gblup_variances_all_11001_12419) + +saveRDS(T17_7_gblup_prediction_all,"T17_7_gblup_prediction_all.rds") +saveRDS(T17_7_gblup_variances_all,"T17_7_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_7_gfblup_prediction_all_1_1000=readRDS(file="T17_7_gfblup_prediction_all_1_1000.rds") +T17_7_gfblup_prediction_all_1001_2000=readRDS(file="T17_7_gfblup_prediction_all_1001_2000.rds") +T17_7_gfblup_prediction_all_2001_3000=readRDS(file="T17_7_gfblup_prediction_all_2001_3000.rds") +T17_7_gfblup_prediction_all_3001_4000=readRDS(file="T17_7_gfblup_prediction_all_3001_4000.rds") +T17_7_gfblup_prediction_all_4001_5000=readRDS(file="T17_7_gfblup_prediction_all_4001_5000.rds") +T17_7_gfblup_prediction_all_5001_6000=readRDS(file="T17_7_gfblup_prediction_all_5001_6000.rds") +T17_7_gfblup_prediction_all_6001_7000=readRDS(file="T17_7_gfblup_prediction_all_6001_7000.rds") +T17_7_gfblup_prediction_all_7001_8000=readRDS(file="T17_7_gfblup_prediction_all_7001_8000.rds") +T17_7_gfblup_prediction_all_8001_9000=readRDS(file="T17_7_gfblup_prediction_all_8001_9000.rds") +T17_7_gfblup_prediction_all_9001_10000=readRDS(file="T17_7_gfblup_prediction_all_9001_10000.rds") +T17_7_gfblup_prediction_all_10001_11000=readRDS(file="T17_7_gfblup_prediction_all_10001_11000.rds") +T17_7_gfblup_prediction_all_11001_12419=readRDS(file="T17_7_gfblup_prediction_all_11001_12419.rds") + +T17_7_gfblup_variances_all_1_1000=readRDS(file="T17_7_gfblup_variances_all_1_1000.rds") +T17_7_gfblup_variances_all_1001_2000=readRDS(file="T17_7_gfblup_variances_all_1001_2000.rds") +T17_7_gfblup_variances_all_2001_3000=readRDS(file="T17_7_gfblup_variances_all_2001_3000.rds") +T17_7_gfblup_variances_all_3001_4000=readRDS(file="T17_7_gfblup_variances_all_3001_4000.rds") +T17_7_gfblup_variances_all_4001_5000=readRDS(file="T17_7_gfblup_variances_all_4001_5000.rds") +T17_7_gfblup_variances_all_5001_6000=readRDS(file="T17_7_gfblup_variances_all_5001_6000.rds") +T17_7_gfblup_variances_all_6001_7000=readRDS(file="T17_7_gfblup_variances_all_6001_7000.rds") +T17_7_gfblup_variances_all_7001_8000=readRDS(file="T17_7_gfblup_variances_all_7001_8000.rds") +T17_7_gfblup_variances_all_8001_9000=readRDS(file="T17_7_gfblup_variances_all_8001_9000.rds") +T17_7_gfblup_variances_all_9001_10000=readRDS(file="T17_7_gfblup_variances_all_9001_10000.rds") +T17_7_gfblup_variances_all_10001_11000=readRDS(file="T17_7_gfblup_variances_all_10001_11000.rds") +T17_7_gfblup_variances_all_11001_12419=readRDS(file="T17_7_gfblup_variances_all_11001_12419.rds") + +cycles=length(T17_7_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T17_7_gfblup_variances_all=rep(list(list()),cycles) +T17_7_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_1_1000[[r]]) + T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_1001_2000[[r]]) + T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_2001_3000[[r]]) + T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_3001_4000[[r]]) + T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_4001_5000[[r]]) + T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_5001_6000[[r]]) + T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_6001_7000[[r]]) + T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_7001_8000[[r]]) + T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_8001_9000[[r]]) + T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_9001_10000[[r]]) + T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_10001_11000[[r]]) + T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_11001_12419[[r]]) + + T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_1_1000[[r]]) + T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_1001_2000[[r]]) + T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_2001_3000[[r]]) + T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_3001_4000[[r]]) + T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_4001_5000[[r]]) + T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_5001_6000[[r]]) + T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_6001_7000[[r]]) + T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_7001_8000[[r]]) + T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_8001_9000[[r]]) + T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_9001_10000[[r]]) + T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_10001_11000[[r]]) + T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T17_7_gfblup_prediction_all,"T17_7_gfblup_prediction_all.rds") +saveRDS(T17_7_gfblup_variances_all,"T17_7_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_8_gblup_prediction_all_1_1000=readRDS(file="T17_8_gblup_prediction_all_1_1000.rds") +T17_8_gblup_prediction_all_1001_2000=readRDS(file="T17_8_gblup_prediction_all_1001_2000.rds") +T17_8_gblup_prediction_all_2001_3000=readRDS(file="T17_8_gblup_prediction_all_2001_3000.rds") +T17_8_gblup_prediction_all_3001_4000=readRDS(file="T17_8_gblup_prediction_all_3001_4000.rds") +T17_8_gblup_prediction_all_4001_5000=readRDS(file="T17_8_gblup_prediction_all_4001_5000.rds") +T17_8_gblup_prediction_all_5001_6000=readRDS(file="T17_8_gblup_prediction_all_5001_6000.rds") +T17_8_gblup_prediction_all_6001_7000=readRDS(file="T17_8_gblup_prediction_all_6001_7000.rds") +T17_8_gblup_prediction_all_7001_8000=readRDS(file="T17_8_gblup_prediction_all_7001_8000.rds") +T17_8_gblup_prediction_all_8001_9000=readRDS(file="T17_8_gblup_prediction_all_8001_9000.rds") +T17_8_gblup_prediction_all_9001_10000=readRDS(file="T17_8_gblup_prediction_all_9001_10000.rds") +T17_8_gblup_prediction_all_10001_11000=readRDS(file="T17_8_gblup_prediction_all_10001_11000.rds") +T17_8_gblup_prediction_all_11001_12419=readRDS(file="T17_8_gblup_prediction_all_11001_12419.rds") +T17_8_gblup_prediction_all=c(T17_8_gblup_prediction_all_1_1000,T17_8_gblup_prediction_all_1001_2000,T17_8_gblup_prediction_all_2001_3000,T17_8_gblup_prediction_all_3001_4000,T17_8_gblup_prediction_all_4001_5000,T17_8_gblup_prediction_all_5001_6000,T17_8_gblup_prediction_all_6001_7000,T17_8_gblup_prediction_all_7001_8000,T17_8_gblup_prediction_all_8001_9000,T17_8_gblup_prediction_all_9001_10000,T17_8_gblup_prediction_all_10001_11000,T17_8_gblup_prediction_all_11001_12419) + +T17_8_gblup_variances_all_1_1000=readRDS(file="T17_8_gblup_variances_all_1_1000.rds") +T17_8_gblup_variances_all_1001_2000=readRDS(file="T17_8_gblup_variances_all_1001_2000.rds") +T17_8_gblup_variances_all_2001_3000=readRDS(file="T17_8_gblup_variances_all_2001_3000.rds") +T17_8_gblup_variances_all_3001_4000=readRDS(file="T17_8_gblup_variances_all_3001_4000.rds") +T17_8_gblup_variances_all_4001_5000=readRDS(file="T17_8_gblup_variances_all_4001_5000.rds") +T17_8_gblup_variances_all_5001_6000=readRDS(file="T17_8_gblup_variances_all_5001_6000.rds") +T17_8_gblup_variances_all_6001_7000=readRDS(file="T17_8_gblup_variances_all_6001_7000.rds") +T17_8_gblup_variances_all_7001_8000=readRDS(file="T17_8_gblup_variances_all_7001_8000.rds") +T17_8_gblup_variances_all_8001_9000=readRDS(file="T17_8_gblup_variances_all_8001_9000.rds") +T17_8_gblup_variances_all_9001_10000=readRDS(file="T17_8_gblup_variances_all_9001_10000.rds") +T17_8_gblup_variances_all_10001_11000=readRDS(file="T17_8_gblup_variances_all_10001_11000.rds") +T17_8_gblup_variances_all_11001_12419=readRDS(file="T17_8_gblup_variances_all_11001_12419.rds") +T17_8_gblup_variances_all=c(T17_8_gblup_variances_all_1_1000,T17_8_gblup_variances_all_1001_2000,T17_8_gblup_variances_all_2001_3000,T17_8_gblup_variances_all_3001_4000,T17_8_gblup_variances_all_4001_5000,T17_8_gblup_variances_all_5001_6000,T17_8_gblup_variances_all_6001_7000,T17_8_gblup_variances_all_7001_8000,T17_8_gblup_variances_all_8001_9000,T17_8_gblup_variances_all_9001_10000,T17_8_gblup_variances_all_10001_11000,T17_8_gblup_variances_all_11001_12419) + +saveRDS(T17_8_gblup_prediction_all,"T17_8_gblup_prediction_all.rds") +saveRDS(T17_8_gblup_variances_all,"T17_8_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_8_gfblup_prediction_all_1_1000=readRDS(file="T17_8_gfblup_prediction_all_1_1000.rds") +T17_8_gfblup_prediction_all_1001_2000=readRDS(file="T17_8_gfblup_prediction_all_1001_2000.rds") +T17_8_gfblup_prediction_all_2001_3000=readRDS(file="T17_8_gfblup_prediction_all_2001_3000.rds") +T17_8_gfblup_prediction_all_3001_4000=readRDS(file="T17_8_gfblup_prediction_all_3001_4000.rds") +T17_8_gfblup_prediction_all_4001_5000=readRDS(file="T17_8_gfblup_prediction_all_4001_5000.rds") +T17_8_gfblup_prediction_all_5001_6000=readRDS(file="T17_8_gfblup_prediction_all_5001_6000.rds") +T17_8_gfblup_prediction_all_6001_7000=readRDS(file="T17_8_gfblup_prediction_all_6001_7000.rds") +T17_8_gfblup_prediction_all_7001_8000=readRDS(file="T17_8_gfblup_prediction_all_7001_8000.rds") +T17_8_gfblup_prediction_all_8001_9000=readRDS(file="T17_8_gfblup_prediction_all_8001_9000.rds") +T17_8_gfblup_prediction_all_9001_10000=readRDS(file="T17_8_gfblup_prediction_all_9001_10000.rds") +T17_8_gfblup_prediction_all_10001_11000=readRDS(file="T17_8_gfblup_prediction_all_10001_11000.rds") +T17_8_gfblup_prediction_all_11001_12419=readRDS(file="T17_8_gfblup_prediction_all_11001_12419.rds") + +T17_8_gfblup_variances_all_1_1000=readRDS(file="T17_8_gfblup_variances_all_1_1000.rds") +T17_8_gfblup_variances_all_1001_2000=readRDS(file="T17_8_gfblup_variances_all_1001_2000.rds") +T17_8_gfblup_variances_all_2001_3000=readRDS(file="T17_8_gfblup_variances_all_2001_3000.rds") +T17_8_gfblup_variances_all_3001_4000=readRDS(file="T17_8_gfblup_variances_all_3001_4000.rds") +T17_8_gfblup_variances_all_4001_5000=readRDS(file="T17_8_gfblup_variances_all_4001_5000.rds") +T17_8_gfblup_variances_all_5001_6000=readRDS(file="T17_8_gfblup_variances_all_5001_6000.rds") +T17_8_gfblup_variances_all_6001_7000=readRDS(file="T17_8_gfblup_variances_all_6001_7000.rds") +T17_8_gfblup_variances_all_7001_8000=readRDS(file="T17_8_gfblup_variances_all_7001_8000.rds") +T17_8_gfblup_variances_all_8001_9000=readRDS(file="T17_8_gfblup_variances_all_8001_9000.rds") +T17_8_gfblup_variances_all_9001_10000=readRDS(file="T17_8_gfblup_variances_all_9001_10000.rds") +T17_8_gfblup_variances_all_10001_11000=readRDS(file="T17_8_gfblup_variances_all_10001_11000.rds") +T17_8_gfblup_variances_all_11001_12419=readRDS(file="T17_8_gfblup_variances_all_11001_12419.rds") + +cycles=length(T17_8_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T17_8_gfblup_variances_all=rep(list(list()),cycles) +T17_8_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_1_1000[[r]]) + T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_1001_2000[[r]]) + T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_2001_3000[[r]]) + T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_3001_4000[[r]]) + T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_4001_5000[[r]]) + T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_5001_6000[[r]]) + T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_6001_7000[[r]]) + T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_7001_8000[[r]]) + T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_8001_9000[[r]]) + T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_9001_10000[[r]]) + T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_10001_11000[[r]]) + T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_11001_12419[[r]]) + + T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_1_1000[[r]]) + T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_1001_2000[[r]]) + T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_2001_3000[[r]]) + T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_3001_4000[[r]]) + T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_4001_5000[[r]]) + T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_5001_6000[[r]]) + T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_6001_7000[[r]]) + T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_7001_8000[[r]]) + T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_8001_9000[[r]]) + T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_9001_10000[[r]]) + T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_10001_11000[[r]]) + T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T17_8_gfblup_prediction_all,"T17_8_gfblup_prediction_all.rds") +saveRDS(T17_8_gfblup_variances_all,"T17_8_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_1_gblup_prediction_all_1_1000=readRDS(file="T18_1_gblup_prediction_all_1_1000.rds") +T18_1_gblup_prediction_all_1001_2000=readRDS(file="T18_1_gblup_prediction_all_1001_2000.rds") +T18_1_gblup_prediction_all_2001_3000=readRDS(file="T18_1_gblup_prediction_all_2001_3000.rds") +T18_1_gblup_prediction_all_3001_4000=readRDS(file="T18_1_gblup_prediction_all_3001_4000.rds") +T18_1_gblup_prediction_all_4001_5000=readRDS(file="T18_1_gblup_prediction_all_4001_5000.rds") +T18_1_gblup_prediction_all_5001_6000=readRDS(file="T18_1_gblup_prediction_all_5001_6000.rds") +T18_1_gblup_prediction_all_6001_7000=readRDS(file="T18_1_gblup_prediction_all_6001_7000.rds") +T18_1_gblup_prediction_all_7001_8000=readRDS(file="T18_1_gblup_prediction_all_7001_8000.rds") +T18_1_gblup_prediction_all_8001_9000=readRDS(file="T18_1_gblup_prediction_all_8001_9000.rds") +T18_1_gblup_prediction_all_9001_10000=readRDS(file="T18_1_gblup_prediction_all_9001_10000.rds") +T18_1_gblup_prediction_all_10001_11000=readRDS(file="T18_1_gblup_prediction_all_10001_11000.rds") +T18_1_gblup_prediction_all_11001_12419=readRDS(file="T18_1_gblup_prediction_all_11001_12419.rds") +T18_1_gblup_prediction_all=c(T18_1_gblup_prediction_all_1_1000,T18_1_gblup_prediction_all_1001_2000,T18_1_gblup_prediction_all_2001_3000,T18_1_gblup_prediction_all_3001_4000,T18_1_gblup_prediction_all_4001_5000,T18_1_gblup_prediction_all_5001_6000,T18_1_gblup_prediction_all_6001_7000,T18_1_gblup_prediction_all_7001_8000,T18_1_gblup_prediction_all_8001_9000,T18_1_gblup_prediction_all_9001_10000,T18_1_gblup_prediction_all_10001_11000,T18_1_gblup_prediction_all_11001_12419) + +T18_1_gblup_variances_all_1_1000=readRDS(file="T18_1_gblup_variances_all_1_1000.rds") +T18_1_gblup_variances_all_1001_2000=readRDS(file="T18_1_gblup_variances_all_1001_2000.rds") +T18_1_gblup_variances_all_2001_3000=readRDS(file="T18_1_gblup_variances_all_2001_3000.rds") +T18_1_gblup_variances_all_3001_4000=readRDS(file="T18_1_gblup_variances_all_3001_4000.rds") +T18_1_gblup_variances_all_4001_5000=readRDS(file="T18_1_gblup_variances_all_4001_5000.rds") +T18_1_gblup_variances_all_5001_6000=readRDS(file="T18_1_gblup_variances_all_5001_6000.rds") +T18_1_gblup_variances_all_6001_7000=readRDS(file="T18_1_gblup_variances_all_6001_7000.rds") +T18_1_gblup_variances_all_7001_8000=readRDS(file="T18_1_gblup_variances_all_7001_8000.rds") +T18_1_gblup_variances_all_8001_9000=readRDS(file="T18_1_gblup_variances_all_8001_9000.rds") +T18_1_gblup_variances_all_9001_10000=readRDS(file="T18_1_gblup_variances_all_9001_10000.rds") +T18_1_gblup_variances_all_10001_11000=readRDS(file="T18_1_gblup_variances_all_10001_11000.rds") +T18_1_gblup_variances_all_11001_12419=readRDS(file="T18_1_gblup_variances_all_11001_12419.rds") +T18_1_gblup_variances_all=c(T18_1_gblup_variances_all_1_1000,T18_1_gblup_variances_all_1001_2000,T18_1_gblup_variances_all_2001_3000,T18_1_gblup_variances_all_3001_4000,T18_1_gblup_variances_all_4001_5000,T18_1_gblup_variances_all_5001_6000,T18_1_gblup_variances_all_6001_7000,T18_1_gblup_variances_all_7001_8000,T18_1_gblup_variances_all_8001_9000,T18_1_gblup_variances_all_9001_10000,T18_1_gblup_variances_all_10001_11000,T18_1_gblup_variances_all_11001_12419) + +saveRDS(T18_1_gblup_prediction_all,"T18_1_gblup_prediction_all.rds") +saveRDS(T18_1_gblup_variances_all,"T18_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_1_gfblup_prediction_all_1_1000=readRDS(file="T18_1_gfblup_prediction_all_1_1000.rds") +T18_1_gfblup_prediction_all_1001_2000=readRDS(file="T18_1_gfblup_prediction_all_1001_2000.rds") +T18_1_gfblup_prediction_all_2001_3000=readRDS(file="T18_1_gfblup_prediction_all_2001_3000.rds") +T18_1_gfblup_prediction_all_3001_4000=readRDS(file="T18_1_gfblup_prediction_all_3001_4000.rds") +T18_1_gfblup_prediction_all_4001_5000=readRDS(file="T18_1_gfblup_prediction_all_4001_5000.rds") +T18_1_gfblup_prediction_all_5001_6000=readRDS(file="T18_1_gfblup_prediction_all_5001_6000.rds") +T18_1_gfblup_prediction_all_6001_7000=readRDS(file="T18_1_gfblup_prediction_all_6001_7000.rds") +T18_1_gfblup_prediction_all_7001_8000=readRDS(file="T18_1_gfblup_prediction_all_7001_8000.rds") +T18_1_gfblup_prediction_all_8001_9000=readRDS(file="T18_1_gfblup_prediction_all_8001_9000.rds") +T18_1_gfblup_prediction_all_9001_10000=readRDS(file="T18_1_gfblup_prediction_all_9001_10000.rds") +T18_1_gfblup_prediction_all_10001_11000=readRDS(file="T18_1_gfblup_prediction_all_10001_11000.rds") +T18_1_gfblup_prediction_all_11001_12419=readRDS(file="T18_1_gfblup_prediction_all_11001_12419.rds") + +T18_1_gfblup_variances_all_1_1000=readRDS(file="T18_1_gfblup_variances_all_1_1000.rds") +T18_1_gfblup_variances_all_1001_2000=readRDS(file="T18_1_gfblup_variances_all_1001_2000.rds") +T18_1_gfblup_variances_all_2001_3000=readRDS(file="T18_1_gfblup_variances_all_2001_3000.rds") +T18_1_gfblup_variances_all_3001_4000=readRDS(file="T18_1_gfblup_variances_all_3001_4000.rds") +T18_1_gfblup_variances_all_4001_5000=readRDS(file="T18_1_gfblup_variances_all_4001_5000.rds") +T18_1_gfblup_variances_all_5001_6000=readRDS(file="T18_1_gfblup_variances_all_5001_6000.rds") +T18_1_gfblup_variances_all_6001_7000=readRDS(file="T18_1_gfblup_variances_all_6001_7000.rds") +T18_1_gfblup_variances_all_7001_8000=readRDS(file="T18_1_gfblup_variances_all_7001_8000.rds") +T18_1_gfblup_variances_all_8001_9000=readRDS(file="T18_1_gfblup_variances_all_8001_9000.rds") +T18_1_gfblup_variances_all_9001_10000=readRDS(file="T18_1_gfblup_variances_all_9001_10000.rds") +T18_1_gfblup_variances_all_10001_11000=readRDS(file="T18_1_gfblup_variances_all_10001_11000.rds") +T18_1_gfblup_variances_all_11001_12419=readRDS(file="T18_1_gfblup_variances_all_11001_12419.rds") + +cycles=length(T18_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T18_1_gfblup_variances_all=rep(list(list()),cycles) +T18_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_1_1000[[r]]) + T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_1001_2000[[r]]) + T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_2001_3000[[r]]) + T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_3001_4000[[r]]) + T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_4001_5000[[r]]) + T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_5001_6000[[r]]) + T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_6001_7000[[r]]) + T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_7001_8000[[r]]) + T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_8001_9000[[r]]) + T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_9001_10000[[r]]) + T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_10001_11000[[r]]) + T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_11001_12419[[r]]) + + T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_1_1000[[r]]) + T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_1001_2000[[r]]) + T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_2001_3000[[r]]) + T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_3001_4000[[r]]) + T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_4001_5000[[r]]) + T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_5001_6000[[r]]) + T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_6001_7000[[r]]) + T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_7001_8000[[r]]) + T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_8001_9000[[r]]) + T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_9001_10000[[r]]) + T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_10001_11000[[r]]) + T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T18_1_gfblup_prediction_all,"T18_1_gfblup_prediction_all.rds") +saveRDS(T18_1_gfblup_variances_all,"T18_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_2_gblup_prediction_all_1_1000=readRDS(file="T18_2_gblup_prediction_all_1_1000.rds") +T18_2_gblup_prediction_all_1001_2000=readRDS(file="T18_2_gblup_prediction_all_1001_2000.rds") +T18_2_gblup_prediction_all_2001_3000=readRDS(file="T18_2_gblup_prediction_all_2001_3000.rds") +T18_2_gblup_prediction_all_3001_4000=readRDS(file="T18_2_gblup_prediction_all_3001_4000.rds") +T18_2_gblup_prediction_all_4001_5000=readRDS(file="T18_2_gblup_prediction_all_4001_5000.rds") +T18_2_gblup_prediction_all_5001_6000=readRDS(file="T18_2_gblup_prediction_all_5001_6000.rds") +T18_2_gblup_prediction_all_6001_7000=readRDS(file="T18_2_gblup_prediction_all_6001_7000.rds") +T18_2_gblup_prediction_all_7001_8000=readRDS(file="T18_2_gblup_prediction_all_7001_8000.rds") +T18_2_gblup_prediction_all_8001_9000=readRDS(file="T18_2_gblup_prediction_all_8001_9000.rds") +T18_2_gblup_prediction_all_9001_10000=readRDS(file="T18_2_gblup_prediction_all_9001_10000.rds") +T18_2_gblup_prediction_all_10001_11000=readRDS(file="T18_2_gblup_prediction_all_10001_11000.rds") +T18_2_gblup_prediction_all_11001_12419=readRDS(file="T18_2_gblup_prediction_all_11001_12419.rds") +T18_2_gblup_prediction_all=c(T18_2_gblup_prediction_all_1_1000,T18_2_gblup_prediction_all_1001_2000,T18_2_gblup_prediction_all_2001_3000,T18_2_gblup_prediction_all_3001_4000,T18_2_gblup_prediction_all_4001_5000,T18_2_gblup_prediction_all_5001_6000,T18_2_gblup_prediction_all_6001_7000,T18_2_gblup_prediction_all_7001_8000,T18_2_gblup_prediction_all_8001_9000,T18_2_gblup_prediction_all_9001_10000,T18_2_gblup_prediction_all_10001_11000,T18_2_gblup_prediction_all_11001_12419) + +T18_2_gblup_variances_all_1_1000=readRDS(file="T18_2_gblup_variances_all_1_1000.rds") +T18_2_gblup_variances_all_1001_2000=readRDS(file="T18_2_gblup_variances_all_1001_2000.rds") +T18_2_gblup_variances_all_2001_3000=readRDS(file="T18_2_gblup_variances_all_2001_3000.rds") +T18_2_gblup_variances_all_3001_4000=readRDS(file="T18_2_gblup_variances_all_3001_4000.rds") +T18_2_gblup_variances_all_4001_5000=readRDS(file="T18_2_gblup_variances_all_4001_5000.rds") +T18_2_gblup_variances_all_5001_6000=readRDS(file="T18_2_gblup_variances_all_5001_6000.rds") +T18_2_gblup_variances_all_6001_7000=readRDS(file="T18_2_gblup_variances_all_6001_7000.rds") +T18_2_gblup_variances_all_7001_8000=readRDS(file="T18_2_gblup_variances_all_7001_8000.rds") +T18_2_gblup_variances_all_8001_9000=readRDS(file="T18_2_gblup_variances_all_8001_9000.rds") +T18_2_gblup_variances_all_9001_10000=readRDS(file="T18_2_gblup_variances_all_9001_10000.rds") +T18_2_gblup_variances_all_10001_11000=readRDS(file="T18_2_gblup_variances_all_10001_11000.rds") +T18_2_gblup_variances_all_11001_12419=readRDS(file="T18_2_gblup_variances_all_11001_12419.rds") +T18_2_gblup_variances_all=c(T18_2_gblup_variances_all_1_1000,T18_2_gblup_variances_all_1001_2000,T18_2_gblup_variances_all_2001_3000,T18_2_gblup_variances_all_3001_4000,T18_2_gblup_variances_all_4001_5000,T18_2_gblup_variances_all_5001_6000,T18_2_gblup_variances_all_6001_7000,T18_2_gblup_variances_all_7001_8000,T18_2_gblup_variances_all_8001_9000,T18_2_gblup_variances_all_9001_10000,T18_2_gblup_variances_all_10001_11000,T18_2_gblup_variances_all_11001_12419) + +saveRDS(T18_2_gblup_prediction_all,"T18_2_gblup_prediction_all.rds") +saveRDS(T18_2_gblup_variances_all,"T18_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_2_gfblup_prediction_all_1_1000=readRDS(file="T18_2_gfblup_prediction_all_1_1000.rds") +T18_2_gfblup_prediction_all_1001_2000=readRDS(file="T18_2_gfblup_prediction_all_1001_2000.rds") +T18_2_gfblup_prediction_all_2001_3000=readRDS(file="T18_2_gfblup_prediction_all_2001_3000.rds") +T18_2_gfblup_prediction_all_3001_4000=readRDS(file="T18_2_gfblup_prediction_all_3001_4000.rds") +T18_2_gfblup_prediction_all_4001_5000=readRDS(file="T18_2_gfblup_prediction_all_4001_5000.rds") +T18_2_gfblup_prediction_all_5001_6000=readRDS(file="T18_2_gfblup_prediction_all_5001_6000.rds") +T18_2_gfblup_prediction_all_6001_7000=readRDS(file="T18_2_gfblup_prediction_all_6001_7000.rds") +T18_2_gfblup_prediction_all_7001_8000=readRDS(file="T18_2_gfblup_prediction_all_7001_8000.rds") +T18_2_gfblup_prediction_all_8001_9000=readRDS(file="T18_2_gfblup_prediction_all_8001_9000.rds") +T18_2_gfblup_prediction_all_9001_10000=readRDS(file="T18_2_gfblup_prediction_all_9001_10000.rds") +T18_2_gfblup_prediction_all_10001_11000=readRDS(file="T18_2_gfblup_prediction_all_10001_11000.rds") +T18_2_gfblup_prediction_all_11001_12419=readRDS(file="T18_2_gfblup_prediction_all_11001_12419.rds") + +T18_2_gfblup_variances_all_1_1000=readRDS(file="T18_2_gfblup_variances_all_1_1000.rds") +T18_2_gfblup_variances_all_1001_2000=readRDS(file="T18_2_gfblup_variances_all_1001_2000.rds") +T18_2_gfblup_variances_all_2001_3000=readRDS(file="T18_2_gfblup_variances_all_2001_3000.rds") +T18_2_gfblup_variances_all_3001_4000=readRDS(file="T18_2_gfblup_variances_all_3001_4000.rds") +T18_2_gfblup_variances_all_4001_5000=readRDS(file="T18_2_gfblup_variances_all_4001_5000.rds") +T18_2_gfblup_variances_all_5001_6000=readRDS(file="T18_2_gfblup_variances_all_5001_6000.rds") +T18_2_gfblup_variances_all_6001_7000=readRDS(file="T18_2_gfblup_variances_all_6001_7000.rds") +T18_2_gfblup_variances_all_7001_8000=readRDS(file="T18_2_gfblup_variances_all_7001_8000.rds") +T18_2_gfblup_variances_all_8001_9000=readRDS(file="T18_2_gfblup_variances_all_8001_9000.rds") +T18_2_gfblup_variances_all_9001_10000=readRDS(file="T18_2_gfblup_variances_all_9001_10000.rds") +T18_2_gfblup_variances_all_10001_11000=readRDS(file="T18_2_gfblup_variances_all_10001_11000.rds") +T18_2_gfblup_variances_all_11001_12419=readRDS(file="T18_2_gfblup_variances_all_11001_12419.rds") + +cycles=length(T18_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T18_2_gfblup_variances_all=rep(list(list()),cycles) +T18_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_1_1000[[r]]) + T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_1001_2000[[r]]) + T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_2001_3000[[r]]) + T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_3001_4000[[r]]) + T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_4001_5000[[r]]) + T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_5001_6000[[r]]) + T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_6001_7000[[r]]) + T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_7001_8000[[r]]) + T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_8001_9000[[r]]) + T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_9001_10000[[r]]) + T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_10001_11000[[r]]) + T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_11001_12419[[r]]) + + T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_1_1000[[r]]) + T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_1001_2000[[r]]) + T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_2001_3000[[r]]) + T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_3001_4000[[r]]) + T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_4001_5000[[r]]) + T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_5001_6000[[r]]) + T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_6001_7000[[r]]) + T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_7001_8000[[r]]) + T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_8001_9000[[r]]) + T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_9001_10000[[r]]) + T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_10001_11000[[r]]) + T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T18_2_gfblup_prediction_all,"T18_2_gfblup_prediction_all.rds") +saveRDS(T18_2_gfblup_variances_all,"T18_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_3_gblup_prediction_all_1_1000=readRDS(file="T18_3_gblup_prediction_all_1_1000.rds") +T18_3_gblup_prediction_all_1001_2000=readRDS(file="T18_3_gblup_prediction_all_1001_2000.rds") +T18_3_gblup_prediction_all_2001_3000=readRDS(file="T18_3_gblup_prediction_all_2001_3000.rds") +T18_3_gblup_prediction_all_3001_4000=readRDS(file="T18_3_gblup_prediction_all_3001_4000.rds") +T18_3_gblup_prediction_all_4001_5000=readRDS(file="T18_3_gblup_prediction_all_4001_5000.rds") +T18_3_gblup_prediction_all_5001_6000=readRDS(file="T18_3_gblup_prediction_all_5001_6000.rds") +T18_3_gblup_prediction_all_6001_7000=readRDS(file="T18_3_gblup_prediction_all_6001_7000.rds") +T18_3_gblup_prediction_all_7001_8000=readRDS(file="T18_3_gblup_prediction_all_7001_8000.rds") +T18_3_gblup_prediction_all_8001_9000=readRDS(file="T18_3_gblup_prediction_all_8001_9000.rds") +T18_3_gblup_prediction_all_9001_10000=readRDS(file="T18_3_gblup_prediction_all_9001_10000.rds") +T18_3_gblup_prediction_all_10001_11000=readRDS(file="T18_3_gblup_prediction_all_10001_11000.rds") +T18_3_gblup_prediction_all_11001_12419=readRDS(file="T18_3_gblup_prediction_all_11001_12419.rds") +T18_3_gblup_prediction_all=c(T18_3_gblup_prediction_all_1_1000,T18_3_gblup_prediction_all_1001_2000,T18_3_gblup_prediction_all_2001_3000,T18_3_gblup_prediction_all_3001_4000,T18_3_gblup_prediction_all_4001_5000,T18_3_gblup_prediction_all_5001_6000,T18_3_gblup_prediction_all_6001_7000,T18_3_gblup_prediction_all_7001_8000,T18_3_gblup_prediction_all_8001_9000,T18_3_gblup_prediction_all_9001_10000,T18_3_gblup_prediction_all_10001_11000,T18_3_gblup_prediction_all_11001_12419) + +T18_3_gblup_variances_all_1_1000=readRDS(file="T18_3_gblup_variances_all_1_1000.rds") +T18_3_gblup_variances_all_1001_2000=readRDS(file="T18_3_gblup_variances_all_1001_2000.rds") +T18_3_gblup_variances_all_2001_3000=readRDS(file="T18_3_gblup_variances_all_2001_3000.rds") +T18_3_gblup_variances_all_3001_4000=readRDS(file="T18_3_gblup_variances_all_3001_4000.rds") +T18_3_gblup_variances_all_4001_5000=readRDS(file="T18_3_gblup_variances_all_4001_5000.rds") +T18_3_gblup_variances_all_5001_6000=readRDS(file="T18_3_gblup_variances_all_5001_6000.rds") +T18_3_gblup_variances_all_6001_7000=readRDS(file="T18_3_gblup_variances_all_6001_7000.rds") +T18_3_gblup_variances_all_7001_8000=readRDS(file="T18_3_gblup_variances_all_7001_8000.rds") +T18_3_gblup_variances_all_8001_9000=readRDS(file="T18_3_gblup_variances_all_8001_9000.rds") +T18_3_gblup_variances_all_9001_10000=readRDS(file="T18_3_gblup_variances_all_9001_10000.rds") +T18_3_gblup_variances_all_10001_11000=readRDS(file="T18_3_gblup_variances_all_10001_11000.rds") +T18_3_gblup_variances_all_11001_12419=readRDS(file="T18_3_gblup_variances_all_11001_12419.rds") +T18_3_gblup_variances_all=c(T18_3_gblup_variances_all_1_1000,T18_3_gblup_variances_all_1001_2000,T18_3_gblup_variances_all_2001_3000,T18_3_gblup_variances_all_3001_4000,T18_3_gblup_variances_all_4001_5000,T18_3_gblup_variances_all_5001_6000,T18_3_gblup_variances_all_6001_7000,T18_3_gblup_variances_all_7001_8000,T18_3_gblup_variances_all_8001_9000,T18_3_gblup_variances_all_9001_10000,T18_3_gblup_variances_all_10001_11000,T18_3_gblup_variances_all_11001_12419) + +saveRDS(T18_3_gblup_prediction_all,"T18_3_gblup_prediction_all.rds") +saveRDS(T18_3_gblup_variances_all,"T18_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_3_gfblup_prediction_all_1_1000=readRDS(file="T18_3_gfblup_prediction_all_1_1000.rds") +T18_3_gfblup_prediction_all_1001_2000=readRDS(file="T18_3_gfblup_prediction_all_1001_2000.rds") +T18_3_gfblup_prediction_all_2001_3000=readRDS(file="T18_3_gfblup_prediction_all_2001_3000.rds") +T18_3_gfblup_prediction_all_3001_4000=readRDS(file="T18_3_gfblup_prediction_all_3001_4000.rds") +T18_3_gfblup_prediction_all_4001_5000=readRDS(file="T18_3_gfblup_prediction_all_4001_5000.rds") +T18_3_gfblup_prediction_all_5001_6000=readRDS(file="T18_3_gfblup_prediction_all_5001_6000.rds") +T18_3_gfblup_prediction_all_6001_7000=readRDS(file="T18_3_gfblup_prediction_all_6001_7000.rds") +T18_3_gfblup_prediction_all_7001_8000=readRDS(file="T18_3_gfblup_prediction_all_7001_8000.rds") +T18_3_gfblup_prediction_all_8001_9000=readRDS(file="T18_3_gfblup_prediction_all_8001_9000.rds") +T18_3_gfblup_prediction_all_9001_10000=readRDS(file="T18_3_gfblup_prediction_all_9001_10000.rds") +T18_3_gfblup_prediction_all_10001_11000=readRDS(file="T18_3_gfblup_prediction_all_10001_11000.rds") +T18_3_gfblup_prediction_all_11001_12419=readRDS(file="T18_3_gfblup_prediction_all_11001_12419.rds") + +T18_3_gfblup_variances_all_1_1000=readRDS(file="T18_3_gfblup_variances_all_1_1000.rds") +T18_3_gfblup_variances_all_1001_2000=readRDS(file="T18_3_gfblup_variances_all_1001_2000.rds") +T18_3_gfblup_variances_all_2001_3000=readRDS(file="T18_3_gfblup_variances_all_2001_3000.rds") +T18_3_gfblup_variances_all_3001_4000=readRDS(file="T18_3_gfblup_variances_all_3001_4000.rds") +T18_3_gfblup_variances_all_4001_5000=readRDS(file="T18_3_gfblup_variances_all_4001_5000.rds") +T18_3_gfblup_variances_all_5001_6000=readRDS(file="T18_3_gfblup_variances_all_5001_6000.rds") +T18_3_gfblup_variances_all_6001_7000=readRDS(file="T18_3_gfblup_variances_all_6001_7000.rds") +T18_3_gfblup_variances_all_7001_8000=readRDS(file="T18_3_gfblup_variances_all_7001_8000.rds") +T18_3_gfblup_variances_all_8001_9000=readRDS(file="T18_3_gfblup_variances_all_8001_9000.rds") +T18_3_gfblup_variances_all_9001_10000=readRDS(file="T18_3_gfblup_variances_all_9001_10000.rds") +T18_3_gfblup_variances_all_10001_11000=readRDS(file="T18_3_gfblup_variances_all_10001_11000.rds") +T18_3_gfblup_variances_all_11001_12419=readRDS(file="T18_3_gfblup_variances_all_11001_12419.rds") + +cycles=length(T18_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T18_3_gfblup_variances_all=rep(list(list()),cycles) +T18_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_1_1000[[r]]) + T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_1001_2000[[r]]) + T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_2001_3000[[r]]) + T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_3001_4000[[r]]) + T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_4001_5000[[r]]) + T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_5001_6000[[r]]) + T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_6001_7000[[r]]) + T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_7001_8000[[r]]) + T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_8001_9000[[r]]) + T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_9001_10000[[r]]) + T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_10001_11000[[r]]) + T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_11001_12419[[r]]) + + T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_1_1000[[r]]) + T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_1001_2000[[r]]) + T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_2001_3000[[r]]) + T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_3001_4000[[r]]) + T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_4001_5000[[r]]) + T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_5001_6000[[r]]) + T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_6001_7000[[r]]) + T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_7001_8000[[r]]) + T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_8001_9000[[r]]) + T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_9001_10000[[r]]) + T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_10001_11000[[r]]) + T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T18_3_gfblup_prediction_all,"T18_3_gfblup_prediction_all.rds") +saveRDS(T18_3_gfblup_variances_all,"T18_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_4_gblup_prediction_all_1_1000=readRDS(file="T18_4_gblup_prediction_all_1_1000.rds") +T18_4_gblup_prediction_all_1001_2000=readRDS(file="T18_4_gblup_prediction_all_1001_2000.rds") +T18_4_gblup_prediction_all_2001_3000=readRDS(file="T18_4_gblup_prediction_all_2001_3000.rds") +T18_4_gblup_prediction_all_3001_4000=readRDS(file="T18_4_gblup_prediction_all_3001_4000.rds") +T18_4_gblup_prediction_all_4001_5000=readRDS(file="T18_4_gblup_prediction_all_4001_5000.rds") +T18_4_gblup_prediction_all_5001_6000=readRDS(file="T18_4_gblup_prediction_all_5001_6000.rds") +T18_4_gblup_prediction_all_6001_7000=readRDS(file="T18_4_gblup_prediction_all_6001_7000.rds") +T18_4_gblup_prediction_all_7001_8000=readRDS(file="T18_4_gblup_prediction_all_7001_8000.rds") +T18_4_gblup_prediction_all_8001_9000=readRDS(file="T18_4_gblup_prediction_all_8001_9000.rds") +T18_4_gblup_prediction_all_9001_10000=readRDS(file="T18_4_gblup_prediction_all_9001_10000.rds") +T18_4_gblup_prediction_all_10001_11000=readRDS(file="T18_4_gblup_prediction_all_10001_11000.rds") +T18_4_gblup_prediction_all_11001_12419=readRDS(file="T18_4_gblup_prediction_all_11001_12419.rds") +T18_4_gblup_prediction_all=c(T18_4_gblup_prediction_all_1_1000,T18_4_gblup_prediction_all_1001_2000,T18_4_gblup_prediction_all_2001_3000,T18_4_gblup_prediction_all_3001_4000,T18_4_gblup_prediction_all_4001_5000,T18_4_gblup_prediction_all_5001_6000,T18_4_gblup_prediction_all_6001_7000,T18_4_gblup_prediction_all_7001_8000,T18_4_gblup_prediction_all_8001_9000,T18_4_gblup_prediction_all_9001_10000,T18_4_gblup_prediction_all_10001_11000,T18_4_gblup_prediction_all_11001_12419) + +T18_4_gblup_variances_all_1_1000=readRDS(file="T18_4_gblup_variances_all_1_1000.rds") +T18_4_gblup_variances_all_1001_2000=readRDS(file="T18_4_gblup_variances_all_1001_2000.rds") +T18_4_gblup_variances_all_2001_3000=readRDS(file="T18_4_gblup_variances_all_2001_3000.rds") +T18_4_gblup_variances_all_3001_4000=readRDS(file="T18_4_gblup_variances_all_3001_4000.rds") +T18_4_gblup_variances_all_4001_5000=readRDS(file="T18_4_gblup_variances_all_4001_5000.rds") +T18_4_gblup_variances_all_5001_6000=readRDS(file="T18_4_gblup_variances_all_5001_6000.rds") +T18_4_gblup_variances_all_6001_7000=readRDS(file="T18_4_gblup_variances_all_6001_7000.rds") +T18_4_gblup_variances_all_7001_8000=readRDS(file="T18_4_gblup_variances_all_7001_8000.rds") +T18_4_gblup_variances_all_8001_9000=readRDS(file="T18_4_gblup_variances_all_8001_9000.rds") +T18_4_gblup_variances_all_9001_10000=readRDS(file="T18_4_gblup_variances_all_9001_10000.rds") +T18_4_gblup_variances_all_10001_11000=readRDS(file="T18_4_gblup_variances_all_10001_11000.rds") +T18_4_gblup_variances_all_11001_12419=readRDS(file="T18_4_gblup_variances_all_11001_12419.rds") +T18_4_gblup_variances_all=c(T18_4_gblup_variances_all_1_1000,T18_4_gblup_variances_all_1001_2000,T18_4_gblup_variances_all_2001_3000,T18_4_gblup_variances_all_3001_4000,T18_4_gblup_variances_all_4001_5000,T18_4_gblup_variances_all_5001_6000,T18_4_gblup_variances_all_6001_7000,T18_4_gblup_variances_all_7001_8000,T18_4_gblup_variances_all_8001_9000,T18_4_gblup_variances_all_9001_10000,T18_4_gblup_variances_all_10001_11000,T18_4_gblup_variances_all_11001_12419) + +saveRDS(T18_4_gblup_prediction_all,"T18_4_gblup_prediction_all.rds") +saveRDS(T18_4_gblup_variances_all,"T18_4_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_4_gfblup_prediction_all_1_1000=readRDS(file="T18_4_gfblup_prediction_all_1_1000.rds") +T18_4_gfblup_prediction_all_1001_2000=readRDS(file="T18_4_gfblup_prediction_all_1001_2000.rds") +T18_4_gfblup_prediction_all_2001_3000=readRDS(file="T18_4_gfblup_prediction_all_2001_3000.rds") +T18_4_gfblup_prediction_all_3001_4000=readRDS(file="T18_4_gfblup_prediction_all_3001_4000.rds") +T18_4_gfblup_prediction_all_4001_5000=readRDS(file="T18_4_gfblup_prediction_all_4001_5000.rds") +T18_4_gfblup_prediction_all_5001_6000=readRDS(file="T18_4_gfblup_prediction_all_5001_6000.rds") +T18_4_gfblup_prediction_all_6001_7000=readRDS(file="T18_4_gfblup_prediction_all_6001_7000.rds") +T18_4_gfblup_prediction_all_7001_8000=readRDS(file="T18_4_gfblup_prediction_all_7001_8000.rds") +T18_4_gfblup_prediction_all_8001_9000=readRDS(file="T18_4_gfblup_prediction_all_8001_9000.rds") +T18_4_gfblup_prediction_all_9001_10000=readRDS(file="T18_4_gfblup_prediction_all_9001_10000.rds") +T18_4_gfblup_prediction_all_10001_11000=readRDS(file="T18_4_gfblup_prediction_all_10001_11000.rds") +T18_4_gfblup_prediction_all_11001_12419=readRDS(file="T18_4_gfblup_prediction_all_11001_12419.rds") + +T18_4_gfblup_variances_all_1_1000=readRDS(file="T18_4_gfblup_variances_all_1_1000.rds") +T18_4_gfblup_variances_all_1001_2000=readRDS(file="T18_4_gfblup_variances_all_1001_2000.rds") +T18_4_gfblup_variances_all_2001_3000=readRDS(file="T18_4_gfblup_variances_all_2001_3000.rds") +T18_4_gfblup_variances_all_3001_4000=readRDS(file="T18_4_gfblup_variances_all_3001_4000.rds") +T18_4_gfblup_variances_all_4001_5000=readRDS(file="T18_4_gfblup_variances_all_4001_5000.rds") +T18_4_gfblup_variances_all_5001_6000=readRDS(file="T18_4_gfblup_variances_all_5001_6000.rds") +T18_4_gfblup_variances_all_6001_7000=readRDS(file="T18_4_gfblup_variances_all_6001_7000.rds") +T18_4_gfblup_variances_all_7001_8000=readRDS(file="T18_4_gfblup_variances_all_7001_8000.rds") +T18_4_gfblup_variances_all_8001_9000=readRDS(file="T18_4_gfblup_variances_all_8001_9000.rds") +T18_4_gfblup_variances_all_9001_10000=readRDS(file="T18_4_gfblup_variances_all_9001_10000.rds") +T18_4_gfblup_variances_all_10001_11000=readRDS(file="T18_4_gfblup_variances_all_10001_11000.rds") +T18_4_gfblup_variances_all_11001_12419=readRDS(file="T18_4_gfblup_variances_all_11001_12419.rds") + +cycles=length(T18_4_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T18_4_gfblup_variances_all=rep(list(list()),cycles) +T18_4_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_1_1000[[r]]) + T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_1001_2000[[r]]) + T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_2001_3000[[r]]) + T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_3001_4000[[r]]) + T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_4001_5000[[r]]) + T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_5001_6000[[r]]) + T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_6001_7000[[r]]) + T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_7001_8000[[r]]) + T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_8001_9000[[r]]) + T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_9001_10000[[r]]) + T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_10001_11000[[r]]) + T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_11001_12419[[r]]) + + T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_1_1000[[r]]) + T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_1001_2000[[r]]) + T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_2001_3000[[r]]) + T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_3001_4000[[r]]) + T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_4001_5000[[r]]) + T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_5001_6000[[r]]) + T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_6001_7000[[r]]) + T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_7001_8000[[r]]) + T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_8001_9000[[r]]) + T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_9001_10000[[r]]) + T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_10001_11000[[r]]) + T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T18_4_gfblup_prediction_all,"T18_4_gfblup_prediction_all.rds") +saveRDS(T18_4_gfblup_variances_all,"T18_4_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_5_gblup_prediction_all_1_1000=readRDS(file="T18_5_gblup_prediction_all_1_1000.rds") +T18_5_gblup_prediction_all_1001_2000=readRDS(file="T18_5_gblup_prediction_all_1001_2000.rds") +T18_5_gblup_prediction_all_2001_3000=readRDS(file="T18_5_gblup_prediction_all_2001_3000.rds") +T18_5_gblup_prediction_all_3001_4000=readRDS(file="T18_5_gblup_prediction_all_3001_4000.rds") +T18_5_gblup_prediction_all_4001_5000=readRDS(file="T18_5_gblup_prediction_all_4001_5000.rds") +T18_5_gblup_prediction_all_5001_6000=readRDS(file="T18_5_gblup_prediction_all_5001_6000.rds") +T18_5_gblup_prediction_all_6001_7000=readRDS(file="T18_5_gblup_prediction_all_6001_7000.rds") +T18_5_gblup_prediction_all_7001_8000=readRDS(file="T18_5_gblup_prediction_all_7001_8000.rds") +T18_5_gblup_prediction_all_8001_9000=readRDS(file="T18_5_gblup_prediction_all_8001_9000.rds") +T18_5_gblup_prediction_all_9001_10000=readRDS(file="T18_5_gblup_prediction_all_9001_10000.rds") +T18_5_gblup_prediction_all_10001_11000=readRDS(file="T18_5_gblup_prediction_all_10001_11000.rds") +T18_5_gblup_prediction_all_11001_12419=readRDS(file="T18_5_gblup_prediction_all_11001_12419.rds") +T18_5_gblup_prediction_all=c(T18_5_gblup_prediction_all_1_1000,T18_5_gblup_prediction_all_1001_2000,T18_5_gblup_prediction_all_2001_3000,T18_5_gblup_prediction_all_3001_4000,T18_5_gblup_prediction_all_4001_5000,T18_5_gblup_prediction_all_5001_6000,T18_5_gblup_prediction_all_6001_7000,T18_5_gblup_prediction_all_7001_8000,T18_5_gblup_prediction_all_8001_9000,T18_5_gblup_prediction_all_9001_10000,T18_5_gblup_prediction_all_10001_11000,T18_5_gblup_prediction_all_11001_12419) + +T18_5_gblup_variances_all_1_1000=readRDS(file="T18_5_gblup_variances_all_1_1000.rds") +T18_5_gblup_variances_all_1001_2000=readRDS(file="T18_5_gblup_variances_all_1001_2000.rds") +T18_5_gblup_variances_all_2001_3000=readRDS(file="T18_5_gblup_variances_all_2001_3000.rds") +T18_5_gblup_variances_all_3001_4000=readRDS(file="T18_5_gblup_variances_all_3001_4000.rds") +T18_5_gblup_variances_all_4001_5000=readRDS(file="T18_5_gblup_variances_all_4001_5000.rds") +T18_5_gblup_variances_all_5001_6000=readRDS(file="T18_5_gblup_variances_all_5001_6000.rds") +T18_5_gblup_variances_all_6001_7000=readRDS(file="T18_5_gblup_variances_all_6001_7000.rds") +T18_5_gblup_variances_all_7001_8000=readRDS(file="T18_5_gblup_variances_all_7001_8000.rds") +T18_5_gblup_variances_all_8001_9000=readRDS(file="T18_5_gblup_variances_all_8001_9000.rds") +T18_5_gblup_variances_all_9001_10000=readRDS(file="T18_5_gblup_variances_all_9001_10000.rds") +T18_5_gblup_variances_all_10001_11000=readRDS(file="T18_5_gblup_variances_all_10001_11000.rds") +T18_5_gblup_variances_all_11001_12419=readRDS(file="T18_5_gblup_variances_all_11001_12419.rds") +T18_5_gblup_variances_all=c(T18_5_gblup_variances_all_1_1000,T18_5_gblup_variances_all_1001_2000,T18_5_gblup_variances_all_2001_3000,T18_5_gblup_variances_all_3001_4000,T18_5_gblup_variances_all_4001_5000,T18_5_gblup_variances_all_5001_6000,T18_5_gblup_variances_all_6001_7000,T18_5_gblup_variances_all_7001_8000,T18_5_gblup_variances_all_8001_9000,T18_5_gblup_variances_all_9001_10000,T18_5_gblup_variances_all_10001_11000,T18_5_gblup_variances_all_11001_12419) + +saveRDS(T18_5_gblup_prediction_all,"T18_5_gblup_prediction_all.rds") +saveRDS(T18_5_gblup_variances_all,"T18_5_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_5_gfblup_prediction_all_1_1000=readRDS(file="T18_5_gfblup_prediction_all_1_1000.rds") +T18_5_gfblup_prediction_all_1001_2000=readRDS(file="T18_5_gfblup_prediction_all_1001_2000.rds") +T18_5_gfblup_prediction_all_2001_3000=readRDS(file="T18_5_gfblup_prediction_all_2001_3000.rds") +T18_5_gfblup_prediction_all_3001_4000=readRDS(file="T18_5_gfblup_prediction_all_3001_4000.rds") +T18_5_gfblup_prediction_all_4001_5000=readRDS(file="T18_5_gfblup_prediction_all_4001_5000.rds") +T18_5_gfblup_prediction_all_5001_6000=readRDS(file="T18_5_gfblup_prediction_all_5001_6000.rds") +T18_5_gfblup_prediction_all_6001_7000=readRDS(file="T18_5_gfblup_prediction_all_6001_7000.rds") +T18_5_gfblup_prediction_all_7001_8000=readRDS(file="T18_5_gfblup_prediction_all_7001_8000.rds") +T18_5_gfblup_prediction_all_8001_9000=readRDS(file="T18_5_gfblup_prediction_all_8001_9000.rds") +T18_5_gfblup_prediction_all_9001_10000=readRDS(file="T18_5_gfblup_prediction_all_9001_10000.rds") +T18_5_gfblup_prediction_all_10001_11000=readRDS(file="T18_5_gfblup_prediction_all_10001_11000.rds") +T18_5_gfblup_prediction_all_11001_12419=readRDS(file="T18_5_gfblup_prediction_all_11001_12419.rds") + +T18_5_gfblup_variances_all_1_1000=readRDS(file="T18_5_gfblup_variances_all_1_1000.rds") +T18_5_gfblup_variances_all_1001_2000=readRDS(file="T18_5_gfblup_variances_all_1001_2000.rds") +T18_5_gfblup_variances_all_2001_3000=readRDS(file="T18_5_gfblup_variances_all_2001_3000.rds") +T18_5_gfblup_variances_all_3001_4000=readRDS(file="T18_5_gfblup_variances_all_3001_4000.rds") +T18_5_gfblup_variances_all_4001_5000=readRDS(file="T18_5_gfblup_variances_all_4001_5000.rds") +T18_5_gfblup_variances_all_5001_6000=readRDS(file="T18_5_gfblup_variances_all_5001_6000.rds") +T18_5_gfblup_variances_all_6001_7000=readRDS(file="T18_5_gfblup_variances_all_6001_7000.rds") +T18_5_gfblup_variances_all_7001_8000=readRDS(file="T18_5_gfblup_variances_all_7001_8000.rds") +T18_5_gfblup_variances_all_8001_9000=readRDS(file="T18_5_gfblup_variances_all_8001_9000.rds") +T18_5_gfblup_variances_all_9001_10000=readRDS(file="T18_5_gfblup_variances_all_9001_10000.rds") +T18_5_gfblup_variances_all_10001_11000=readRDS(file="T18_5_gfblup_variances_all_10001_11000.rds") +T18_5_gfblup_variances_all_11001_12419=readRDS(file="T18_5_gfblup_variances_all_11001_12419.rds") + +cycles=length(T18_5_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T18_5_gfblup_variances_all=rep(list(list()),cycles) +T18_5_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_1_1000[[r]]) + T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_1001_2000[[r]]) + T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_2001_3000[[r]]) + T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_3001_4000[[r]]) + T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_4001_5000[[r]]) + T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_5001_6000[[r]]) + T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_6001_7000[[r]]) + T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_7001_8000[[r]]) + T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_8001_9000[[r]]) + T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_9001_10000[[r]]) + T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_10001_11000[[r]]) + T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_11001_12419[[r]]) + + T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_1_1000[[r]]) + T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_1001_2000[[r]]) + T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_2001_3000[[r]]) + T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_3001_4000[[r]]) + T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_4001_5000[[r]]) + T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_5001_6000[[r]]) + T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_6001_7000[[r]]) + T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_7001_8000[[r]]) + T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_8001_9000[[r]]) + T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_9001_10000[[r]]) + T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_10001_11000[[r]]) + T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T18_5_gfblup_prediction_all,"T18_5_gfblup_prediction_all.rds") +saveRDS(T18_5_gfblup_variances_all,"T18_5_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_6_gblup_prediction_all_1_1000=readRDS(file="T18_6_gblup_prediction_all_1_1000.rds") +T18_6_gblup_prediction_all_1001_2000=readRDS(file="T18_6_gblup_prediction_all_1001_2000.rds") +T18_6_gblup_prediction_all_2001_3000=readRDS(file="T18_6_gblup_prediction_all_2001_3000.rds") +T18_6_gblup_prediction_all_3001_4000=readRDS(file="T18_6_gblup_prediction_all_3001_4000.rds") +T18_6_gblup_prediction_all_4001_5000=readRDS(file="T18_6_gblup_prediction_all_4001_5000.rds") +T18_6_gblup_prediction_all_5001_6000=readRDS(file="T18_6_gblup_prediction_all_5001_6000.rds") +T18_6_gblup_prediction_all_6001_7000=readRDS(file="T18_6_gblup_prediction_all_6001_7000.rds") +T18_6_gblup_prediction_all_7001_8000=readRDS(file="T18_6_gblup_prediction_all_7001_8000.rds") +T18_6_gblup_prediction_all_8001_9000=readRDS(file="T18_6_gblup_prediction_all_8001_9000.rds") +T18_6_gblup_prediction_all_9001_10000=readRDS(file="T18_6_gblup_prediction_all_9001_10000.rds") +T18_6_gblup_prediction_all_10001_11000=readRDS(file="T18_6_gblup_prediction_all_10001_11000.rds") +T18_6_gblup_prediction_all_11001_12419=readRDS(file="T18_6_gblup_prediction_all_11001_12419.rds") +T18_6_gblup_prediction_all=c(T18_6_gblup_prediction_all_1_1000,T18_6_gblup_prediction_all_1001_2000,T18_6_gblup_prediction_all_2001_3000,T18_6_gblup_prediction_all_3001_4000,T18_6_gblup_prediction_all_4001_5000,T18_6_gblup_prediction_all_5001_6000,T18_6_gblup_prediction_all_6001_7000,T18_6_gblup_prediction_all_7001_8000,T18_6_gblup_prediction_all_8001_9000,T18_6_gblup_prediction_all_9001_10000,T18_6_gblup_prediction_all_10001_11000,T18_6_gblup_prediction_all_11001_12419) + +T18_6_gblup_variances_all_1_1000=readRDS(file="T18_6_gblup_variances_all_1_1000.rds") +T18_6_gblup_variances_all_1001_2000=readRDS(file="T18_6_gblup_variances_all_1001_2000.rds") +T18_6_gblup_variances_all_2001_3000=readRDS(file="T18_6_gblup_variances_all_2001_3000.rds") +T18_6_gblup_variances_all_3001_4000=readRDS(file="T18_6_gblup_variances_all_3001_4000.rds") +T18_6_gblup_variances_all_4001_5000=readRDS(file="T18_6_gblup_variances_all_4001_5000.rds") +T18_6_gblup_variances_all_5001_6000=readRDS(file="T18_6_gblup_variances_all_5001_6000.rds") +T18_6_gblup_variances_all_6001_7000=readRDS(file="T18_6_gblup_variances_all_6001_7000.rds") +T18_6_gblup_variances_all_7001_8000=readRDS(file="T18_6_gblup_variances_all_7001_8000.rds") +T18_6_gblup_variances_all_8001_9000=readRDS(file="T18_6_gblup_variances_all_8001_9000.rds") +T18_6_gblup_variances_all_9001_10000=readRDS(file="T18_6_gblup_variances_all_9001_10000.rds") +T18_6_gblup_variances_all_10001_11000=readRDS(file="T18_6_gblup_variances_all_10001_11000.rds") +T18_6_gblup_variances_all_11001_12419=readRDS(file="T18_6_gblup_variances_all_11001_12419.rds") +T18_6_gblup_variances_all=c(T18_6_gblup_variances_all_1_1000,T18_6_gblup_variances_all_1001_2000,T18_6_gblup_variances_all_2001_3000,T18_6_gblup_variances_all_3001_4000,T18_6_gblup_variances_all_4001_5000,T18_6_gblup_variances_all_5001_6000,T18_6_gblup_variances_all_6001_7000,T18_6_gblup_variances_all_7001_8000,T18_6_gblup_variances_all_8001_9000,T18_6_gblup_variances_all_9001_10000,T18_6_gblup_variances_all_10001_11000,T18_6_gblup_variances_all_11001_12419) + +saveRDS(T18_6_gblup_prediction_all,"T18_6_gblup_prediction_all.rds") +saveRDS(T18_6_gblup_variances_all,"T18_6_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_6_gfblup_prediction_all_1_1000=readRDS(file="T18_6_gfblup_prediction_all_1_1000.rds") +T18_6_gfblup_prediction_all_1001_2000=readRDS(file="T18_6_gfblup_prediction_all_1001_2000.rds") +T18_6_gfblup_prediction_all_2001_3000=readRDS(file="T18_6_gfblup_prediction_all_2001_3000.rds") +T18_6_gfblup_prediction_all_3001_4000=readRDS(file="T18_6_gfblup_prediction_all_3001_4000.rds") +T18_6_gfblup_prediction_all_4001_5000=readRDS(file="T18_6_gfblup_prediction_all_4001_5000.rds") +T18_6_gfblup_prediction_all_5001_6000=readRDS(file="T18_6_gfblup_prediction_all_5001_6000.rds") +T18_6_gfblup_prediction_all_6001_7000=readRDS(file="T18_6_gfblup_prediction_all_6001_7000.rds") +T18_6_gfblup_prediction_all_7001_8000=readRDS(file="T18_6_gfblup_prediction_all_7001_8000.rds") +T18_6_gfblup_prediction_all_8001_9000=readRDS(file="T18_6_gfblup_prediction_all_8001_9000.rds") +T18_6_gfblup_prediction_all_9001_10000=readRDS(file="T18_6_gfblup_prediction_all_9001_10000.rds") +T18_6_gfblup_prediction_all_10001_11000=readRDS(file="T18_6_gfblup_prediction_all_10001_11000.rds") +T18_6_gfblup_prediction_all_11001_12419=readRDS(file="T18_6_gfblup_prediction_all_11001_12419.rds") + +T18_6_gfblup_variances_all_1_1000=readRDS(file="T18_6_gfblup_variances_all_1_1000.rds") +T18_6_gfblup_variances_all_1001_2000=readRDS(file="T18_6_gfblup_variances_all_1001_2000.rds") +T18_6_gfblup_variances_all_2001_3000=readRDS(file="T18_6_gfblup_variances_all_2001_3000.rds") +T18_6_gfblup_variances_all_3001_4000=readRDS(file="T18_6_gfblup_variances_all_3001_4000.rds") +T18_6_gfblup_variances_all_4001_5000=readRDS(file="T18_6_gfblup_variances_all_4001_5000.rds") +T18_6_gfblup_variances_all_5001_6000=readRDS(file="T18_6_gfblup_variances_all_5001_6000.rds") +T18_6_gfblup_variances_all_6001_7000=readRDS(file="T18_6_gfblup_variances_all_6001_7000.rds") +T18_6_gfblup_variances_all_7001_8000=readRDS(file="T18_6_gfblup_variances_all_7001_8000.rds") +T18_6_gfblup_variances_all_8001_9000=readRDS(file="T18_6_gfblup_variances_all_8001_9000.rds") +T18_6_gfblup_variances_all_9001_10000=readRDS(file="T18_6_gfblup_variances_all_9001_10000.rds") +T18_6_gfblup_variances_all_10001_11000=readRDS(file="T18_6_gfblup_variances_all_10001_11000.rds") +T18_6_gfblup_variances_all_11001_12419=readRDS(file="T18_6_gfblup_variances_all_11001_12419.rds") + +cycles=length(T18_6_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T18_6_gfblup_variances_all=rep(list(list()),cycles) +T18_6_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_1_1000[[r]]) + T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_1001_2000[[r]]) + T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_2001_3000[[r]]) + T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_3001_4000[[r]]) + T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_4001_5000[[r]]) + T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_5001_6000[[r]]) + T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_6001_7000[[r]]) + T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_7001_8000[[r]]) + T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_8001_9000[[r]]) + T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_9001_10000[[r]]) + T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_10001_11000[[r]]) + T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_11001_12419[[r]]) + + T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_1_1000[[r]]) + T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_1001_2000[[r]]) + T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_2001_3000[[r]]) + T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_3001_4000[[r]]) + T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_4001_5000[[r]]) + T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_5001_6000[[r]]) + T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_6001_7000[[r]]) + T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_7001_8000[[r]]) + T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_8001_9000[[r]]) + T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_9001_10000[[r]]) + T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_10001_11000[[r]]) + T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T18_6_gfblup_prediction_all,"T18_6_gfblup_prediction_all.rds") +saveRDS(T18_6_gfblup_variances_all,"T18_6_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_7_gblup_prediction_all_1_1000=readRDS(file="T18_7_gblup_prediction_all_1_1000.rds") +T18_7_gblup_prediction_all_1001_2000=readRDS(file="T18_7_gblup_prediction_all_1001_2000.rds") +T18_7_gblup_prediction_all_2001_3000=readRDS(file="T18_7_gblup_prediction_all_2001_3000.rds") +T18_7_gblup_prediction_all_3001_4000=readRDS(file="T18_7_gblup_prediction_all_3001_4000.rds") +T18_7_gblup_prediction_all_4001_5000=readRDS(file="T18_7_gblup_prediction_all_4001_5000.rds") +T18_7_gblup_prediction_all_5001_6000=readRDS(file="T18_7_gblup_prediction_all_5001_6000.rds") +T18_7_gblup_prediction_all_6001_7000=readRDS(file="T18_7_gblup_prediction_all_6001_7000.rds") +T18_7_gblup_prediction_all_7001_8000=readRDS(file="T18_7_gblup_prediction_all_7001_8000.rds") +T18_7_gblup_prediction_all_8001_9000=readRDS(file="T18_7_gblup_prediction_all_8001_9000.rds") +T18_7_gblup_prediction_all_9001_10000=readRDS(file="T18_7_gblup_prediction_all_9001_10000.rds") +T18_7_gblup_prediction_all_10001_11000=readRDS(file="T18_7_gblup_prediction_all_10001_11000.rds") +T18_7_gblup_prediction_all_11001_12419=readRDS(file="T18_7_gblup_prediction_all_11001_12419.rds") +T18_7_gblup_prediction_all=c(T18_7_gblup_prediction_all_1_1000,T18_7_gblup_prediction_all_1001_2000,T18_7_gblup_prediction_all_2001_3000,T18_7_gblup_prediction_all_3001_4000,T18_7_gblup_prediction_all_4001_5000,T18_7_gblup_prediction_all_5001_6000,T18_7_gblup_prediction_all_6001_7000,T18_7_gblup_prediction_all_7001_8000,T18_7_gblup_prediction_all_8001_9000,T18_7_gblup_prediction_all_9001_10000,T18_7_gblup_prediction_all_10001_11000,T18_7_gblup_prediction_all_11001_12419) + +T18_7_gblup_variances_all_1_1000=readRDS(file="T18_7_gblup_variances_all_1_1000.rds") +T18_7_gblup_variances_all_1001_2000=readRDS(file="T18_7_gblup_variances_all_1001_2000.rds") +T18_7_gblup_variances_all_2001_3000=readRDS(file="T18_7_gblup_variances_all_2001_3000.rds") +T18_7_gblup_variances_all_3001_4000=readRDS(file="T18_7_gblup_variances_all_3001_4000.rds") +T18_7_gblup_variances_all_4001_5000=readRDS(file="T18_7_gblup_variances_all_4001_5000.rds") +T18_7_gblup_variances_all_5001_6000=readRDS(file="T18_7_gblup_variances_all_5001_6000.rds") +T18_7_gblup_variances_all_6001_7000=readRDS(file="T18_7_gblup_variances_all_6001_7000.rds") +T18_7_gblup_variances_all_7001_8000=readRDS(file="T18_7_gblup_variances_all_7001_8000.rds") +T18_7_gblup_variances_all_8001_9000=readRDS(file="T18_7_gblup_variances_all_8001_9000.rds") +T18_7_gblup_variances_all_9001_10000=readRDS(file="T18_7_gblup_variances_all_9001_10000.rds") +T18_7_gblup_variances_all_10001_11000=readRDS(file="T18_7_gblup_variances_all_10001_11000.rds") +T18_7_gblup_variances_all_11001_12419=readRDS(file="T18_7_gblup_variances_all_11001_12419.rds") +T18_7_gblup_variances_all=c(T18_7_gblup_variances_all_1_1000,T18_7_gblup_variances_all_1001_2000,T18_7_gblup_variances_all_2001_3000,T18_7_gblup_variances_all_3001_4000,T18_7_gblup_variances_all_4001_5000,T18_7_gblup_variances_all_5001_6000,T18_7_gblup_variances_all_6001_7000,T18_7_gblup_variances_all_7001_8000,T18_7_gblup_variances_all_8001_9000,T18_7_gblup_variances_all_9001_10000,T18_7_gblup_variances_all_10001_11000,T18_7_gblup_variances_all_11001_12419) + +saveRDS(T18_7_gblup_prediction_all,"T18_7_gblup_prediction_all.rds") +saveRDS(T18_7_gblup_variances_all,"T18_7_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_7_gfblup_prediction_all_1_1000=readRDS(file="T18_7_gfblup_prediction_all_1_1000.rds") +T18_7_gfblup_prediction_all_1001_2000=readRDS(file="T18_7_gfblup_prediction_all_1001_2000.rds") +T18_7_gfblup_prediction_all_2001_3000=readRDS(file="T18_7_gfblup_prediction_all_2001_3000.rds") +T18_7_gfblup_prediction_all_3001_4000=readRDS(file="T18_7_gfblup_prediction_all_3001_4000.rds") +T18_7_gfblup_prediction_all_4001_5000=readRDS(file="T18_7_gfblup_prediction_all_4001_5000.rds") +T18_7_gfblup_prediction_all_5001_6000=readRDS(file="T18_7_gfblup_prediction_all_5001_6000.rds") +T18_7_gfblup_prediction_all_6001_7000=readRDS(file="T18_7_gfblup_prediction_all_6001_7000.rds") +T18_7_gfblup_prediction_all_7001_8000=readRDS(file="T18_7_gfblup_prediction_all_7001_8000.rds") +T18_7_gfblup_prediction_all_8001_9000=readRDS(file="T18_7_gfblup_prediction_all_8001_9000.rds") +T18_7_gfblup_prediction_all_9001_10000=readRDS(file="T18_7_gfblup_prediction_all_9001_10000.rds") +T18_7_gfblup_prediction_all_10001_11000=readRDS(file="T18_7_gfblup_prediction_all_10001_11000.rds") +T18_7_gfblup_prediction_all_11001_12419=readRDS(file="T18_7_gfblup_prediction_all_11001_12419.rds") + +T18_7_gfblup_variances_all_1_1000=readRDS(file="T18_7_gfblup_variances_all_1_1000.rds") +T18_7_gfblup_variances_all_1001_2000=readRDS(file="T18_7_gfblup_variances_all_1001_2000.rds") +T18_7_gfblup_variances_all_2001_3000=readRDS(file="T18_7_gfblup_variances_all_2001_3000.rds") +T18_7_gfblup_variances_all_3001_4000=readRDS(file="T18_7_gfblup_variances_all_3001_4000.rds") +T18_7_gfblup_variances_all_4001_5000=readRDS(file="T18_7_gfblup_variances_all_4001_5000.rds") +T18_7_gfblup_variances_all_5001_6000=readRDS(file="T18_7_gfblup_variances_all_5001_6000.rds") +T18_7_gfblup_variances_all_6001_7000=readRDS(file="T18_7_gfblup_variances_all_6001_7000.rds") +T18_7_gfblup_variances_all_7001_8000=readRDS(file="T18_7_gfblup_variances_all_7001_8000.rds") +T18_7_gfblup_variances_all_8001_9000=readRDS(file="T18_7_gfblup_variances_all_8001_9000.rds") +T18_7_gfblup_variances_all_9001_10000=readRDS(file="T18_7_gfblup_variances_all_9001_10000.rds") +T18_7_gfblup_variances_all_10001_11000=readRDS(file="T18_7_gfblup_variances_all_10001_11000.rds") +T18_7_gfblup_variances_all_11001_12419=readRDS(file="T18_7_gfblup_variances_all_11001_12419.rds") + +cycles=length(T18_7_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T18_7_gfblup_variances_all=rep(list(list()),cycles) +T18_7_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_1_1000[[r]]) + T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_1001_2000[[r]]) + T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_2001_3000[[r]]) + T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_3001_4000[[r]]) + T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_4001_5000[[r]]) + T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_5001_6000[[r]]) + T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_6001_7000[[r]]) + T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_7001_8000[[r]]) + T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_8001_9000[[r]]) + T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_9001_10000[[r]]) + T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_10001_11000[[r]]) + T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_11001_12419[[r]]) + + T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_1_1000[[r]]) + T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_1001_2000[[r]]) + T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_2001_3000[[r]]) + T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_3001_4000[[r]]) + T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_4001_5000[[r]]) + T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_5001_6000[[r]]) + T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_6001_7000[[r]]) + T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_7001_8000[[r]]) + T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_8001_9000[[r]]) + T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_9001_10000[[r]]) + T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_10001_11000[[r]]) + T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T18_7_gfblup_prediction_all,"T18_7_gfblup_prediction_all.rds") +saveRDS(T18_7_gfblup_variances_all,"T18_7_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_8_gblup_prediction_all_1_1000=readRDS(file="T18_8_gblup_prediction_all_1_1000.rds") +T18_8_gblup_prediction_all_1001_2000=readRDS(file="T18_8_gblup_prediction_all_1001_2000.rds") +T18_8_gblup_prediction_all_2001_3000=readRDS(file="T18_8_gblup_prediction_all_2001_3000.rds") +T18_8_gblup_prediction_all_3001_4000=readRDS(file="T18_8_gblup_prediction_all_3001_4000.rds") +T18_8_gblup_prediction_all_4001_5000=readRDS(file="T18_8_gblup_prediction_all_4001_5000.rds") +T18_8_gblup_prediction_all_5001_6000=readRDS(file="T18_8_gblup_prediction_all_5001_6000.rds") +T18_8_gblup_prediction_all_6001_7000=readRDS(file="T18_8_gblup_prediction_all_6001_7000.rds") +T18_8_gblup_prediction_all_7001_8000=readRDS(file="T18_8_gblup_prediction_all_7001_8000.rds") +T18_8_gblup_prediction_all_8001_9000=readRDS(file="T18_8_gblup_prediction_all_8001_9000.rds") +T18_8_gblup_prediction_all_9001_10000=readRDS(file="T18_8_gblup_prediction_all_9001_10000.rds") +T18_8_gblup_prediction_all_10001_11000=readRDS(file="T18_8_gblup_prediction_all_10001_11000.rds") +T18_8_gblup_prediction_all_11001_12419=readRDS(file="T18_8_gblup_prediction_all_11001_12419.rds") +T18_8_gblup_prediction_all=c(T18_8_gblup_prediction_all_1_1000,T18_8_gblup_prediction_all_1001_2000,T18_8_gblup_prediction_all_2001_3000,T18_8_gblup_prediction_all_3001_4000,T18_8_gblup_prediction_all_4001_5000,T18_8_gblup_prediction_all_5001_6000,T18_8_gblup_prediction_all_6001_7000,T18_8_gblup_prediction_all_7001_8000,T18_8_gblup_prediction_all_8001_9000,T18_8_gblup_prediction_all_9001_10000,T18_8_gblup_prediction_all_10001_11000,T18_8_gblup_prediction_all_11001_12419) + +T18_8_gblup_variances_all_1_1000=readRDS(file="T18_8_gblup_variances_all_1_1000.rds") +T18_8_gblup_variances_all_1001_2000=readRDS(file="T18_8_gblup_variances_all_1001_2000.rds") +T18_8_gblup_variances_all_2001_3000=readRDS(file="T18_8_gblup_variances_all_2001_3000.rds") +T18_8_gblup_variances_all_3001_4000=readRDS(file="T18_8_gblup_variances_all_3001_4000.rds") +T18_8_gblup_variances_all_4001_5000=readRDS(file="T18_8_gblup_variances_all_4001_5000.rds") +T18_8_gblup_variances_all_5001_6000=readRDS(file="T18_8_gblup_variances_all_5001_6000.rds") +T18_8_gblup_variances_all_6001_7000=readRDS(file="T18_8_gblup_variances_all_6001_7000.rds") +T18_8_gblup_variances_all_7001_8000=readRDS(file="T18_8_gblup_variances_all_7001_8000.rds") +T18_8_gblup_variances_all_8001_9000=readRDS(file="T18_8_gblup_variances_all_8001_9000.rds") +T18_8_gblup_variances_all_9001_10000=readRDS(file="T18_8_gblup_variances_all_9001_10000.rds") +T18_8_gblup_variances_all_10001_11000=readRDS(file="T18_8_gblup_variances_all_10001_11000.rds") +T18_8_gblup_variances_all_11001_12419=readRDS(file="T18_8_gblup_variances_all_11001_12419.rds") +T18_8_gblup_variances_all=c(T18_8_gblup_variances_all_1_1000,T18_8_gblup_variances_all_1001_2000,T18_8_gblup_variances_all_2001_3000,T18_8_gblup_variances_all_3001_4000,T18_8_gblup_variances_all_4001_5000,T18_8_gblup_variances_all_5001_6000,T18_8_gblup_variances_all_6001_7000,T18_8_gblup_variances_all_7001_8000,T18_8_gblup_variances_all_8001_9000,T18_8_gblup_variances_all_9001_10000,T18_8_gblup_variances_all_10001_11000,T18_8_gblup_variances_all_11001_12419) + +saveRDS(T18_8_gblup_prediction_all,"T18_8_gblup_prediction_all.rds") +saveRDS(T18_8_gblup_variances_all,"T18_8_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_8_gfblup_prediction_all_1_1000=readRDS(file="T18_8_gfblup_prediction_all_1_1000.rds") +T18_8_gfblup_prediction_all_1001_2000=readRDS(file="T18_8_gfblup_prediction_all_1001_2000.rds") +T18_8_gfblup_prediction_all_2001_3000=readRDS(file="T18_8_gfblup_prediction_all_2001_3000.rds") +T18_8_gfblup_prediction_all_3001_4000=readRDS(file="T18_8_gfblup_prediction_all_3001_4000.rds") +T18_8_gfblup_prediction_all_4001_5000=readRDS(file="T18_8_gfblup_prediction_all_4001_5000.rds") +T18_8_gfblup_prediction_all_5001_6000=readRDS(file="T18_8_gfblup_prediction_all_5001_6000.rds") +T18_8_gfblup_prediction_all_6001_7000=readRDS(file="T18_8_gfblup_prediction_all_6001_7000.rds") +T18_8_gfblup_prediction_all_7001_8000=readRDS(file="T18_8_gfblup_prediction_all_7001_8000.rds") +T18_8_gfblup_prediction_all_8001_9000=readRDS(file="T18_8_gfblup_prediction_all_8001_9000.rds") +T18_8_gfblup_prediction_all_9001_10000=readRDS(file="T18_8_gfblup_prediction_all_9001_10000.rds") +T18_8_gfblup_prediction_all_10001_11000=readRDS(file="T18_8_gfblup_prediction_all_10001_11000.rds") +T18_8_gfblup_prediction_all_11001_12419=readRDS(file="T18_8_gfblup_prediction_all_11001_12419.rds") + +T18_8_gfblup_variances_all_1_1000=readRDS(file="T18_8_gfblup_variances_all_1_1000.rds") +T18_8_gfblup_variances_all_1001_2000=readRDS(file="T18_8_gfblup_variances_all_1001_2000.rds") +T18_8_gfblup_variances_all_2001_3000=readRDS(file="T18_8_gfblup_variances_all_2001_3000.rds") +T18_8_gfblup_variances_all_3001_4000=readRDS(file="T18_8_gfblup_variances_all_3001_4000.rds") +T18_8_gfblup_variances_all_4001_5000=readRDS(file="T18_8_gfblup_variances_all_4001_5000.rds") +T18_8_gfblup_variances_all_5001_6000=readRDS(file="T18_8_gfblup_variances_all_5001_6000.rds") +T18_8_gfblup_variances_all_6001_7000=readRDS(file="T18_8_gfblup_variances_all_6001_7000.rds") +T18_8_gfblup_variances_all_7001_8000=readRDS(file="T18_8_gfblup_variances_all_7001_8000.rds") +T18_8_gfblup_variances_all_8001_9000=readRDS(file="T18_8_gfblup_variances_all_8001_9000.rds") +T18_8_gfblup_variances_all_9001_10000=readRDS(file="T18_8_gfblup_variances_all_9001_10000.rds") +T18_8_gfblup_variances_all_10001_11000=readRDS(file="T18_8_gfblup_variances_all_10001_11000.rds") +T18_8_gfblup_variances_all_11001_12419=readRDS(file="T18_8_gfblup_variances_all_11001_12419.rds") + +cycles=length(T18_8_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T18_8_gfblup_variances_all=rep(list(list()),cycles) +T18_8_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_1_1000[[r]]) + T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_1001_2000[[r]]) + T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_2001_3000[[r]]) + T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_3001_4000[[r]]) + T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_4001_5000[[r]]) + T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_5001_6000[[r]]) + T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_6001_7000[[r]]) + T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_7001_8000[[r]]) + T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_8001_9000[[r]]) + T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_9001_10000[[r]]) + T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_10001_11000[[r]]) + T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_11001_12419[[r]]) + + T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_1_1000[[r]]) + T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_1001_2000[[r]]) + T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_2001_3000[[r]]) + T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_3001_4000[[r]]) + T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_4001_5000[[r]]) + T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_5001_6000[[r]]) + T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_6001_7000[[r]]) + T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_7001_8000[[r]]) + T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_8001_9000[[r]]) + T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_9001_10000[[r]]) + T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_10001_11000[[r]]) + T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T18_8_gfblup_prediction_all,"T18_8_gfblup_prediction_all.rds") +saveRDS(T18_8_gfblup_variances_all,"T18_8_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_1_gblup_prediction_all_1_1000=readRDS(file="T19_1_gblup_prediction_all_1_1000.rds") +T19_1_gblup_prediction_all_1001_2000=readRDS(file="T19_1_gblup_prediction_all_1001_2000.rds") +T19_1_gblup_prediction_all_2001_3000=readRDS(file="T19_1_gblup_prediction_all_2001_3000.rds") +T19_1_gblup_prediction_all_3001_4000=readRDS(file="T19_1_gblup_prediction_all_3001_4000.rds") +T19_1_gblup_prediction_all_4001_5000=readRDS(file="T19_1_gblup_prediction_all_4001_5000.rds") +T19_1_gblup_prediction_all_5001_6000=readRDS(file="T19_1_gblup_prediction_all_5001_6000.rds") +T19_1_gblup_prediction_all_6001_7000=readRDS(file="T19_1_gblup_prediction_all_6001_7000.rds") +T19_1_gblup_prediction_all_7001_8000=readRDS(file="T19_1_gblup_prediction_all_7001_8000.rds") +T19_1_gblup_prediction_all_8001_9000=readRDS(file="T19_1_gblup_prediction_all_8001_9000.rds") +T19_1_gblup_prediction_all_9001_10000=readRDS(file="T19_1_gblup_prediction_all_9001_10000.rds") +T19_1_gblup_prediction_all_10001_11000=readRDS(file="T19_1_gblup_prediction_all_10001_11000.rds") +T19_1_gblup_prediction_all_11001_12419=readRDS(file="T19_1_gblup_prediction_all_11001_12419.rds") +T19_1_gblup_prediction_all=c(T19_1_gblup_prediction_all_1_1000,T19_1_gblup_prediction_all_1001_2000,T19_1_gblup_prediction_all_2001_3000,T19_1_gblup_prediction_all_3001_4000,T19_1_gblup_prediction_all_4001_5000,T19_1_gblup_prediction_all_5001_6000,T19_1_gblup_prediction_all_6001_7000,T19_1_gblup_prediction_all_7001_8000,T19_1_gblup_prediction_all_8001_9000,T19_1_gblup_prediction_all_9001_10000,T19_1_gblup_prediction_all_10001_11000,T19_1_gblup_prediction_all_11001_12419) + +T19_1_gblup_variances_all_1_1000=readRDS(file="T19_1_gblup_variances_all_1_1000.rds") +T19_1_gblup_variances_all_1001_2000=readRDS(file="T19_1_gblup_variances_all_1001_2000.rds") +T19_1_gblup_variances_all_2001_3000=readRDS(file="T19_1_gblup_variances_all_2001_3000.rds") +T19_1_gblup_variances_all_3001_4000=readRDS(file="T19_1_gblup_variances_all_3001_4000.rds") +T19_1_gblup_variances_all_4001_5000=readRDS(file="T19_1_gblup_variances_all_4001_5000.rds") +T19_1_gblup_variances_all_5001_6000=readRDS(file="T19_1_gblup_variances_all_5001_6000.rds") +T19_1_gblup_variances_all_6001_7000=readRDS(file="T19_1_gblup_variances_all_6001_7000.rds") +T19_1_gblup_variances_all_7001_8000=readRDS(file="T19_1_gblup_variances_all_7001_8000.rds") +T19_1_gblup_variances_all_8001_9000=readRDS(file="T19_1_gblup_variances_all_8001_9000.rds") +T19_1_gblup_variances_all_9001_10000=readRDS(file="T19_1_gblup_variances_all_9001_10000.rds") +T19_1_gblup_variances_all_10001_11000=readRDS(file="T19_1_gblup_variances_all_10001_11000.rds") +T19_1_gblup_variances_all_11001_12419=readRDS(file="T19_1_gblup_variances_all_11001_12419.rds") +T19_1_gblup_variances_all=c(T19_1_gblup_variances_all_1_1000,T19_1_gblup_variances_all_1001_2000,T19_1_gblup_variances_all_2001_3000,T19_1_gblup_variances_all_3001_4000,T19_1_gblup_variances_all_4001_5000,T19_1_gblup_variances_all_5001_6000,T19_1_gblup_variances_all_6001_7000,T19_1_gblup_variances_all_7001_8000,T19_1_gblup_variances_all_8001_9000,T19_1_gblup_variances_all_9001_10000,T19_1_gblup_variances_all_10001_11000,T19_1_gblup_variances_all_11001_12419) + +saveRDS(T19_1_gblup_prediction_all,"T19_1_gblup_prediction_all.rds") +saveRDS(T19_1_gblup_variances_all,"T19_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_1_gfblup_prediction_all_1_1000=readRDS(file="T19_1_gfblup_prediction_all_1_1000.rds") +T19_1_gfblup_prediction_all_1001_2000=readRDS(file="T19_1_gfblup_prediction_all_1001_2000.rds") +T19_1_gfblup_prediction_all_2001_3000=readRDS(file="T19_1_gfblup_prediction_all_2001_3000.rds") +T19_1_gfblup_prediction_all_3001_4000=readRDS(file="T19_1_gfblup_prediction_all_3001_4000.rds") +T19_1_gfblup_prediction_all_4001_5000=readRDS(file="T19_1_gfblup_prediction_all_4001_5000.rds") +T19_1_gfblup_prediction_all_5001_6000=readRDS(file="T19_1_gfblup_prediction_all_5001_6000.rds") +T19_1_gfblup_prediction_all_6001_7000=readRDS(file="T19_1_gfblup_prediction_all_6001_7000.rds") +T19_1_gfblup_prediction_all_7001_8000=readRDS(file="T19_1_gfblup_prediction_all_7001_8000.rds") +T19_1_gfblup_prediction_all_8001_9000=readRDS(file="T19_1_gfblup_prediction_all_8001_9000.rds") +T19_1_gfblup_prediction_all_9001_10000=readRDS(file="T19_1_gfblup_prediction_all_9001_10000.rds") +T19_1_gfblup_prediction_all_10001_11000=readRDS(file="T19_1_gfblup_prediction_all_10001_11000.rds") +T19_1_gfblup_prediction_all_11001_12419=readRDS(file="T19_1_gfblup_prediction_all_11001_12419.rds") + +T19_1_gfblup_variances_all_1_1000=readRDS(file="T19_1_gfblup_variances_all_1_1000.rds") +T19_1_gfblup_variances_all_1001_2000=readRDS(file="T19_1_gfblup_variances_all_1001_2000.rds") +T19_1_gfblup_variances_all_2001_3000=readRDS(file="T19_1_gfblup_variances_all_2001_3000.rds") +T19_1_gfblup_variances_all_3001_4000=readRDS(file="T19_1_gfblup_variances_all_3001_4000.rds") +T19_1_gfblup_variances_all_4001_5000=readRDS(file="T19_1_gfblup_variances_all_4001_5000.rds") +T19_1_gfblup_variances_all_5001_6000=readRDS(file="T19_1_gfblup_variances_all_5001_6000.rds") +T19_1_gfblup_variances_all_6001_7000=readRDS(file="T19_1_gfblup_variances_all_6001_7000.rds") +T19_1_gfblup_variances_all_7001_8000=readRDS(file="T19_1_gfblup_variances_all_7001_8000.rds") +T19_1_gfblup_variances_all_8001_9000=readRDS(file="T19_1_gfblup_variances_all_8001_9000.rds") +T19_1_gfblup_variances_all_9001_10000=readRDS(file="T19_1_gfblup_variances_all_9001_10000.rds") +T19_1_gfblup_variances_all_10001_11000=readRDS(file="T19_1_gfblup_variances_all_10001_11000.rds") +T19_1_gfblup_variances_all_11001_12419=readRDS(file="T19_1_gfblup_variances_all_11001_12419.rds") + +cycles=length(T19_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T19_1_gfblup_variances_all=rep(list(list()),cycles) +T19_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_1_1000[[r]]) + T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_1001_2000[[r]]) + T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_2001_3000[[r]]) + T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_3001_4000[[r]]) + T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_4001_5000[[r]]) + T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_5001_6000[[r]]) + T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_6001_7000[[r]]) + T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_7001_8000[[r]]) + T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_8001_9000[[r]]) + T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_9001_10000[[r]]) + T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_10001_11000[[r]]) + T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_11001_12419[[r]]) + + T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_1_1000[[r]]) + T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_1001_2000[[r]]) + T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_2001_3000[[r]]) + T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_3001_4000[[r]]) + T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_4001_5000[[r]]) + T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_5001_6000[[r]]) + T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_6001_7000[[r]]) + T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_7001_8000[[r]]) + T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_8001_9000[[r]]) + T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_9001_10000[[r]]) + T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_10001_11000[[r]]) + T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T19_1_gfblup_prediction_all,"T19_1_gfblup_prediction_all.rds") +saveRDS(T19_1_gfblup_variances_all,"T19_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_2_gblup_prediction_all_1_1000=readRDS(file="T19_2_gblup_prediction_all_1_1000.rds") +T19_2_gblup_prediction_all_1001_2000=readRDS(file="T19_2_gblup_prediction_all_1001_2000.rds") +T19_2_gblup_prediction_all_2001_3000=readRDS(file="T19_2_gblup_prediction_all_2001_3000.rds") +T19_2_gblup_prediction_all_3001_4000=readRDS(file="T19_2_gblup_prediction_all_3001_4000.rds") +T19_2_gblup_prediction_all_4001_5000=readRDS(file="T19_2_gblup_prediction_all_4001_5000.rds") +T19_2_gblup_prediction_all_5001_6000=readRDS(file="T19_2_gblup_prediction_all_5001_6000.rds") +T19_2_gblup_prediction_all_6001_7000=readRDS(file="T19_2_gblup_prediction_all_6001_7000.rds") +T19_2_gblup_prediction_all_7001_8000=readRDS(file="T19_2_gblup_prediction_all_7001_8000.rds") +T19_2_gblup_prediction_all_8001_9000=readRDS(file="T19_2_gblup_prediction_all_8001_9000.rds") +T19_2_gblup_prediction_all_9001_10000=readRDS(file="T19_2_gblup_prediction_all_9001_10000.rds") +T19_2_gblup_prediction_all_10001_11000=readRDS(file="T19_2_gblup_prediction_all_10001_11000.rds") +T19_2_gblup_prediction_all_11001_12419=readRDS(file="T19_2_gblup_prediction_all_11001_12419.rds") +T19_2_gblup_prediction_all=c(T19_2_gblup_prediction_all_1_1000,T19_2_gblup_prediction_all_1001_2000,T19_2_gblup_prediction_all_2001_3000,T19_2_gblup_prediction_all_3001_4000,T19_2_gblup_prediction_all_4001_5000,T19_2_gblup_prediction_all_5001_6000,T19_2_gblup_prediction_all_6001_7000,T19_2_gblup_prediction_all_7001_8000,T19_2_gblup_prediction_all_8001_9000,T19_2_gblup_prediction_all_9001_10000,T19_2_gblup_prediction_all_10001_11000,T19_2_gblup_prediction_all_11001_12419) + +T19_2_gblup_variances_all_1_1000=readRDS(file="T19_2_gblup_variances_all_1_1000.rds") +T19_2_gblup_variances_all_1001_2000=readRDS(file="T19_2_gblup_variances_all_1001_2000.rds") +T19_2_gblup_variances_all_2001_3000=readRDS(file="T19_2_gblup_variances_all_2001_3000.rds") +T19_2_gblup_variances_all_3001_4000=readRDS(file="T19_2_gblup_variances_all_3001_4000.rds") +T19_2_gblup_variances_all_4001_5000=readRDS(file="T19_2_gblup_variances_all_4001_5000.rds") +T19_2_gblup_variances_all_5001_6000=readRDS(file="T19_2_gblup_variances_all_5001_6000.rds") +T19_2_gblup_variances_all_6001_7000=readRDS(file="T19_2_gblup_variances_all_6001_7000.rds") +T19_2_gblup_variances_all_7001_8000=readRDS(file="T19_2_gblup_variances_all_7001_8000.rds") +T19_2_gblup_variances_all_8001_9000=readRDS(file="T19_2_gblup_variances_all_8001_9000.rds") +T19_2_gblup_variances_all_9001_10000=readRDS(file="T19_2_gblup_variances_all_9001_10000.rds") +T19_2_gblup_variances_all_10001_11000=readRDS(file="T19_2_gblup_variances_all_10001_11000.rds") +T19_2_gblup_variances_all_11001_12419=readRDS(file="T19_2_gblup_variances_all_11001_12419.rds") +T19_2_gblup_variances_all=c(T19_2_gblup_variances_all_1_1000,T19_2_gblup_variances_all_1001_2000,T19_2_gblup_variances_all_2001_3000,T19_2_gblup_variances_all_3001_4000,T19_2_gblup_variances_all_4001_5000,T19_2_gblup_variances_all_5001_6000,T19_2_gblup_variances_all_6001_7000,T19_2_gblup_variances_all_7001_8000,T19_2_gblup_variances_all_8001_9000,T19_2_gblup_variances_all_9001_10000,T19_2_gblup_variances_all_10001_11000,T19_2_gblup_variances_all_11001_12419) + +saveRDS(T19_2_gblup_prediction_all,"T19_2_gblup_prediction_all.rds") +saveRDS(T19_2_gblup_variances_all,"T19_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_2_gfblup_prediction_all_1_1000=readRDS(file="T19_2_gfblup_prediction_all_1_1000.rds") +T19_2_gfblup_prediction_all_1001_2000=readRDS(file="T19_2_gfblup_prediction_all_1001_2000.rds") +T19_2_gfblup_prediction_all_2001_3000=readRDS(file="T19_2_gfblup_prediction_all_2001_3000.rds") +T19_2_gfblup_prediction_all_3001_4000=readRDS(file="T19_2_gfblup_prediction_all_3001_4000.rds") +T19_2_gfblup_prediction_all_4001_5000=readRDS(file="T19_2_gfblup_prediction_all_4001_5000.rds") +T19_2_gfblup_prediction_all_5001_6000=readRDS(file="T19_2_gfblup_prediction_all_5001_6000.rds") +T19_2_gfblup_prediction_all_6001_7000=readRDS(file="T19_2_gfblup_prediction_all_6001_7000.rds") +T19_2_gfblup_prediction_all_7001_8000=readRDS(file="T19_2_gfblup_prediction_all_7001_8000.rds") +T19_2_gfblup_prediction_all_8001_9000=readRDS(file="T19_2_gfblup_prediction_all_8001_9000.rds") +T19_2_gfblup_prediction_all_9001_10000=readRDS(file="T19_2_gfblup_prediction_all_9001_10000.rds") +T19_2_gfblup_prediction_all_10001_11000=readRDS(file="T19_2_gfblup_prediction_all_10001_11000.rds") +T19_2_gfblup_prediction_all_11001_12419=readRDS(file="T19_2_gfblup_prediction_all_11001_12419.rds") + +T19_2_gfblup_variances_all_1_1000=readRDS(file="T19_2_gfblup_variances_all_1_1000.rds") +T19_2_gfblup_variances_all_1001_2000=readRDS(file="T19_2_gfblup_variances_all_1001_2000.rds") +T19_2_gfblup_variances_all_2001_3000=readRDS(file="T19_2_gfblup_variances_all_2001_3000.rds") +T19_2_gfblup_variances_all_3001_4000=readRDS(file="T19_2_gfblup_variances_all_3001_4000.rds") +T19_2_gfblup_variances_all_4001_5000=readRDS(file="T19_2_gfblup_variances_all_4001_5000.rds") +T19_2_gfblup_variances_all_5001_6000=readRDS(file="T19_2_gfblup_variances_all_5001_6000.rds") +T19_2_gfblup_variances_all_6001_7000=readRDS(file="T19_2_gfblup_variances_all_6001_7000.rds") +T19_2_gfblup_variances_all_7001_8000=readRDS(file="T19_2_gfblup_variances_all_7001_8000.rds") +T19_2_gfblup_variances_all_8001_9000=readRDS(file="T19_2_gfblup_variances_all_8001_9000.rds") +T19_2_gfblup_variances_all_9001_10000=readRDS(file="T19_2_gfblup_variances_all_9001_10000.rds") +T19_2_gfblup_variances_all_10001_11000=readRDS(file="T19_2_gfblup_variances_all_10001_11000.rds") +T19_2_gfblup_variances_all_11001_12419=readRDS(file="T19_2_gfblup_variances_all_11001_12419.rds") + +cycles=length(T19_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T19_2_gfblup_variances_all=rep(list(list()),cycles) +T19_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_1_1000[[r]]) + T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_1001_2000[[r]]) + T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_2001_3000[[r]]) + T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_3001_4000[[r]]) + T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_4001_5000[[r]]) + T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_5001_6000[[r]]) + T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_6001_7000[[r]]) + T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_7001_8000[[r]]) + T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_8001_9000[[r]]) + T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_9001_10000[[r]]) + T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_10001_11000[[r]]) + T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_11001_12419[[r]]) + + T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_1_1000[[r]]) + T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_1001_2000[[r]]) + T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_2001_3000[[r]]) + T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_3001_4000[[r]]) + T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_4001_5000[[r]]) + T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_5001_6000[[r]]) + T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_6001_7000[[r]]) + T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_7001_8000[[r]]) + T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_8001_9000[[r]]) + T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_9001_10000[[r]]) + T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_10001_11000[[r]]) + T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T19_2_gfblup_prediction_all,"T19_2_gfblup_prediction_all.rds") +saveRDS(T19_2_gfblup_variances_all,"T19_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_3_gblup_prediction_all_1_1000=readRDS(file="T19_3_gblup_prediction_all_1_1000.rds") +T19_3_gblup_prediction_all_1001_2000=readRDS(file="T19_3_gblup_prediction_all_1001_2000.rds") +T19_3_gblup_prediction_all_2001_3000=readRDS(file="T19_3_gblup_prediction_all_2001_3000.rds") +T19_3_gblup_prediction_all_3001_4000=readRDS(file="T19_3_gblup_prediction_all_3001_4000.rds") +T19_3_gblup_prediction_all_4001_5000=readRDS(file="T19_3_gblup_prediction_all_4001_5000.rds") +T19_3_gblup_prediction_all_5001_6000=readRDS(file="T19_3_gblup_prediction_all_5001_6000.rds") +T19_3_gblup_prediction_all_6001_7000=readRDS(file="T19_3_gblup_prediction_all_6001_7000.rds") +T19_3_gblup_prediction_all_7001_8000=readRDS(file="T19_3_gblup_prediction_all_7001_8000.rds") +T19_3_gblup_prediction_all_8001_9000=readRDS(file="T19_3_gblup_prediction_all_8001_9000.rds") +T19_3_gblup_prediction_all_9001_10000=readRDS(file="T19_3_gblup_prediction_all_9001_10000.rds") +T19_3_gblup_prediction_all_10001_11000=readRDS(file="T19_3_gblup_prediction_all_10001_11000.rds") +T19_3_gblup_prediction_all_11001_12419=readRDS(file="T19_3_gblup_prediction_all_11001_12419.rds") +T19_3_gblup_prediction_all=c(T19_3_gblup_prediction_all_1_1000,T19_3_gblup_prediction_all_1001_2000,T19_3_gblup_prediction_all_2001_3000,T19_3_gblup_prediction_all_3001_4000,T19_3_gblup_prediction_all_4001_5000,T19_3_gblup_prediction_all_5001_6000,T19_3_gblup_prediction_all_6001_7000,T19_3_gblup_prediction_all_7001_8000,T19_3_gblup_prediction_all_8001_9000,T19_3_gblup_prediction_all_9001_10000,T19_3_gblup_prediction_all_10001_11000,T19_3_gblup_prediction_all_11001_12419) + +T19_3_gblup_variances_all_1_1000=readRDS(file="T19_3_gblup_variances_all_1_1000.rds") +T19_3_gblup_variances_all_1001_2000=readRDS(file="T19_3_gblup_variances_all_1001_2000.rds") +T19_3_gblup_variances_all_2001_3000=readRDS(file="T19_3_gblup_variances_all_2001_3000.rds") +T19_3_gblup_variances_all_3001_4000=readRDS(file="T19_3_gblup_variances_all_3001_4000.rds") +T19_3_gblup_variances_all_4001_5000=readRDS(file="T19_3_gblup_variances_all_4001_5000.rds") +T19_3_gblup_variances_all_5001_6000=readRDS(file="T19_3_gblup_variances_all_5001_6000.rds") +T19_3_gblup_variances_all_6001_7000=readRDS(file="T19_3_gblup_variances_all_6001_7000.rds") +T19_3_gblup_variances_all_7001_8000=readRDS(file="T19_3_gblup_variances_all_7001_8000.rds") +T19_3_gblup_variances_all_8001_9000=readRDS(file="T19_3_gblup_variances_all_8001_9000.rds") +T19_3_gblup_variances_all_9001_10000=readRDS(file="T19_3_gblup_variances_all_9001_10000.rds") +T19_3_gblup_variances_all_10001_11000=readRDS(file="T19_3_gblup_variances_all_10001_11000.rds") +T19_3_gblup_variances_all_11001_12419=readRDS(file="T19_3_gblup_variances_all_11001_12419.rds") +T19_3_gblup_variances_all=c(T19_3_gblup_variances_all_1_1000,T19_3_gblup_variances_all_1001_2000,T19_3_gblup_variances_all_2001_3000,T19_3_gblup_variances_all_3001_4000,T19_3_gblup_variances_all_4001_5000,T19_3_gblup_variances_all_5001_6000,T19_3_gblup_variances_all_6001_7000,T19_3_gblup_variances_all_7001_8000,T19_3_gblup_variances_all_8001_9000,T19_3_gblup_variances_all_9001_10000,T19_3_gblup_variances_all_10001_11000,T19_3_gblup_variances_all_11001_12419) + +saveRDS(T19_3_gblup_prediction_all,"T19_3_gblup_prediction_all.rds") +saveRDS(T19_3_gblup_variances_all,"T19_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_3_gfblup_prediction_all_1_1000=readRDS(file="T19_3_gfblup_prediction_all_1_1000.rds") +T19_3_gfblup_prediction_all_1001_2000=readRDS(file="T19_3_gfblup_prediction_all_1001_2000.rds") +T19_3_gfblup_prediction_all_2001_3000=readRDS(file="T19_3_gfblup_prediction_all_2001_3000.rds") +T19_3_gfblup_prediction_all_3001_4000=readRDS(file="T19_3_gfblup_prediction_all_3001_4000.rds") +T19_3_gfblup_prediction_all_4001_5000=readRDS(file="T19_3_gfblup_prediction_all_4001_5000.rds") +T19_3_gfblup_prediction_all_5001_6000=readRDS(file="T19_3_gfblup_prediction_all_5001_6000.rds") +T19_3_gfblup_prediction_all_6001_7000=readRDS(file="T19_3_gfblup_prediction_all_6001_7000.rds") +T19_3_gfblup_prediction_all_7001_8000=readRDS(file="T19_3_gfblup_prediction_all_7001_8000.rds") +T19_3_gfblup_prediction_all_8001_9000=readRDS(file="T19_3_gfblup_prediction_all_8001_9000.rds") +T19_3_gfblup_prediction_all_9001_10000=readRDS(file="T19_3_gfblup_prediction_all_9001_10000.rds") +T19_3_gfblup_prediction_all_10001_11000=readRDS(file="T19_3_gfblup_prediction_all_10001_11000.rds") +T19_3_gfblup_prediction_all_11001_12419=readRDS(file="T19_3_gfblup_prediction_all_11001_12419.rds") + +T19_3_gfblup_variances_all_1_1000=readRDS(file="T19_3_gfblup_variances_all_1_1000.rds") +T19_3_gfblup_variances_all_1001_2000=readRDS(file="T19_3_gfblup_variances_all_1001_2000.rds") +T19_3_gfblup_variances_all_2001_3000=readRDS(file="T19_3_gfblup_variances_all_2001_3000.rds") +T19_3_gfblup_variances_all_3001_4000=readRDS(file="T19_3_gfblup_variances_all_3001_4000.rds") +T19_3_gfblup_variances_all_4001_5000=readRDS(file="T19_3_gfblup_variances_all_4001_5000.rds") +T19_3_gfblup_variances_all_5001_6000=readRDS(file="T19_3_gfblup_variances_all_5001_6000.rds") +T19_3_gfblup_variances_all_6001_7000=readRDS(file="T19_3_gfblup_variances_all_6001_7000.rds") +T19_3_gfblup_variances_all_7001_8000=readRDS(file="T19_3_gfblup_variances_all_7001_8000.rds") +T19_3_gfblup_variances_all_8001_9000=readRDS(file="T19_3_gfblup_variances_all_8001_9000.rds") +T19_3_gfblup_variances_all_9001_10000=readRDS(file="T19_3_gfblup_variances_all_9001_10000.rds") +T19_3_gfblup_variances_all_10001_11000=readRDS(file="T19_3_gfblup_variances_all_10001_11000.rds") +T19_3_gfblup_variances_all_11001_12419=readRDS(file="T19_3_gfblup_variances_all_11001_12419.rds") + +cycles=length(T19_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T19_3_gfblup_variances_all=rep(list(list()),cycles) +T19_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_1_1000[[r]]) + T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_1001_2000[[r]]) + T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_2001_3000[[r]]) + T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_3001_4000[[r]]) + T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_4001_5000[[r]]) + T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_5001_6000[[r]]) + T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_6001_7000[[r]]) + T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_7001_8000[[r]]) + T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_8001_9000[[r]]) + T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_9001_10000[[r]]) + T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_10001_11000[[r]]) + T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_11001_12419[[r]]) + + T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_1_1000[[r]]) + T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_1001_2000[[r]]) + T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_2001_3000[[r]]) + T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_3001_4000[[r]]) + T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_4001_5000[[r]]) + T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_5001_6000[[r]]) + T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_6001_7000[[r]]) + T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_7001_8000[[r]]) + T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_8001_9000[[r]]) + T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_9001_10000[[r]]) + T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_10001_11000[[r]]) + T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T19_3_gfblup_prediction_all,"T19_3_gfblup_prediction_all.rds") +saveRDS(T19_3_gfblup_variances_all,"T19_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_4_gblup_prediction_all_1_1000=readRDS(file="T19_4_gblup_prediction_all_1_1000.rds") +T19_4_gblup_prediction_all_1001_2000=readRDS(file="T19_4_gblup_prediction_all_1001_2000.rds") +T19_4_gblup_prediction_all_2001_3000=readRDS(file="T19_4_gblup_prediction_all_2001_3000.rds") +T19_4_gblup_prediction_all_3001_4000=readRDS(file="T19_4_gblup_prediction_all_3001_4000.rds") +T19_4_gblup_prediction_all_4001_5000=readRDS(file="T19_4_gblup_prediction_all_4001_5000.rds") +T19_4_gblup_prediction_all_5001_6000=readRDS(file="T19_4_gblup_prediction_all_5001_6000.rds") +T19_4_gblup_prediction_all_6001_7000=readRDS(file="T19_4_gblup_prediction_all_6001_7000.rds") +T19_4_gblup_prediction_all_7001_8000=readRDS(file="T19_4_gblup_prediction_all_7001_8000.rds") +T19_4_gblup_prediction_all_8001_9000=readRDS(file="T19_4_gblup_prediction_all_8001_9000.rds") +T19_4_gblup_prediction_all_9001_10000=readRDS(file="T19_4_gblup_prediction_all_9001_10000.rds") +T19_4_gblup_prediction_all_10001_11000=readRDS(file="T19_4_gblup_prediction_all_10001_11000.rds") +T19_4_gblup_prediction_all_11001_12419=readRDS(file="T19_4_gblup_prediction_all_11001_12419.rds") +T19_4_gblup_prediction_all=c(T19_4_gblup_prediction_all_1_1000,T19_4_gblup_prediction_all_1001_2000,T19_4_gblup_prediction_all_2001_3000,T19_4_gblup_prediction_all_3001_4000,T19_4_gblup_prediction_all_4001_5000,T19_4_gblup_prediction_all_5001_6000,T19_4_gblup_prediction_all_6001_7000,T19_4_gblup_prediction_all_7001_8000,T19_4_gblup_prediction_all_8001_9000,T19_4_gblup_prediction_all_9001_10000,T19_4_gblup_prediction_all_10001_11000,T19_4_gblup_prediction_all_11001_12419) + +T19_4_gblup_variances_all_1_1000=readRDS(file="T19_4_gblup_variances_all_1_1000.rds") +T19_4_gblup_variances_all_1001_2000=readRDS(file="T19_4_gblup_variances_all_1001_2000.rds") +T19_4_gblup_variances_all_2001_3000=readRDS(file="T19_4_gblup_variances_all_2001_3000.rds") +T19_4_gblup_variances_all_3001_4000=readRDS(file="T19_4_gblup_variances_all_3001_4000.rds") +T19_4_gblup_variances_all_4001_5000=readRDS(file="T19_4_gblup_variances_all_4001_5000.rds") +T19_4_gblup_variances_all_5001_6000=readRDS(file="T19_4_gblup_variances_all_5001_6000.rds") +T19_4_gblup_variances_all_6001_7000=readRDS(file="T19_4_gblup_variances_all_6001_7000.rds") +T19_4_gblup_variances_all_7001_8000=readRDS(file="T19_4_gblup_variances_all_7001_8000.rds") +T19_4_gblup_variances_all_8001_9000=readRDS(file="T19_4_gblup_variances_all_8001_9000.rds") +T19_4_gblup_variances_all_9001_10000=readRDS(file="T19_4_gblup_variances_all_9001_10000.rds") +T19_4_gblup_variances_all_10001_11000=readRDS(file="T19_4_gblup_variances_all_10001_11000.rds") +T19_4_gblup_variances_all_11001_12419=readRDS(file="T19_4_gblup_variances_all_11001_12419.rds") +T19_4_gblup_variances_all=c(T19_4_gblup_variances_all_1_1000,T19_4_gblup_variances_all_1001_2000,T19_4_gblup_variances_all_2001_3000,T19_4_gblup_variances_all_3001_4000,T19_4_gblup_variances_all_4001_5000,T19_4_gblup_variances_all_5001_6000,T19_4_gblup_variances_all_6001_7000,T19_4_gblup_variances_all_7001_8000,T19_4_gblup_variances_all_8001_9000,T19_4_gblup_variances_all_9001_10000,T19_4_gblup_variances_all_10001_11000,T19_4_gblup_variances_all_11001_12419) + +saveRDS(T19_4_gblup_prediction_all,"T19_4_gblup_prediction_all.rds") +saveRDS(T19_4_gblup_variances_all,"T19_4_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_4_gfblup_prediction_all_1_1000=readRDS(file="T19_4_gfblup_prediction_all_1_1000.rds") +T19_4_gfblup_prediction_all_1001_2000=readRDS(file="T19_4_gfblup_prediction_all_1001_2000.rds") +T19_4_gfblup_prediction_all_2001_3000=readRDS(file="T19_4_gfblup_prediction_all_2001_3000.rds") +T19_4_gfblup_prediction_all_3001_4000=readRDS(file="T19_4_gfblup_prediction_all_3001_4000.rds") +T19_4_gfblup_prediction_all_4001_5000=readRDS(file="T19_4_gfblup_prediction_all_4001_5000.rds") +T19_4_gfblup_prediction_all_5001_6000=readRDS(file="T19_4_gfblup_prediction_all_5001_6000.rds") +T19_4_gfblup_prediction_all_6001_7000=readRDS(file="T19_4_gfblup_prediction_all_6001_7000.rds") +T19_4_gfblup_prediction_all_7001_8000=readRDS(file="T19_4_gfblup_prediction_all_7001_8000.rds") +T19_4_gfblup_prediction_all_8001_9000=readRDS(file="T19_4_gfblup_prediction_all_8001_9000.rds") +T19_4_gfblup_prediction_all_9001_10000=readRDS(file="T19_4_gfblup_prediction_all_9001_10000.rds") +T19_4_gfblup_prediction_all_10001_11000=readRDS(file="T19_4_gfblup_prediction_all_10001_11000.rds") +T19_4_gfblup_prediction_all_11001_12419=readRDS(file="T19_4_gfblup_prediction_all_11001_12419.rds") + +T19_4_gfblup_variances_all_1_1000=readRDS(file="T19_4_gfblup_variances_all_1_1000.rds") +T19_4_gfblup_variances_all_1001_2000=readRDS(file="T19_4_gfblup_variances_all_1001_2000.rds") +T19_4_gfblup_variances_all_2001_3000=readRDS(file="T19_4_gfblup_variances_all_2001_3000.rds") +T19_4_gfblup_variances_all_3001_4000=readRDS(file="T19_4_gfblup_variances_all_3001_4000.rds") +T19_4_gfblup_variances_all_4001_5000=readRDS(file="T19_4_gfblup_variances_all_4001_5000.rds") +T19_4_gfblup_variances_all_5001_6000=readRDS(file="T19_4_gfblup_variances_all_5001_6000.rds") +T19_4_gfblup_variances_all_6001_7000=readRDS(file="T19_4_gfblup_variances_all_6001_7000.rds") +T19_4_gfblup_variances_all_7001_8000=readRDS(file="T19_4_gfblup_variances_all_7001_8000.rds") +T19_4_gfblup_variances_all_8001_9000=readRDS(file="T19_4_gfblup_variances_all_8001_9000.rds") +T19_4_gfblup_variances_all_9001_10000=readRDS(file="T19_4_gfblup_variances_all_9001_10000.rds") +T19_4_gfblup_variances_all_10001_11000=readRDS(file="T19_4_gfblup_variances_all_10001_11000.rds") +T19_4_gfblup_variances_all_11001_12419=readRDS(file="T19_4_gfblup_variances_all_11001_12419.rds") + +cycles=length(T19_4_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T19_4_gfblup_variances_all=rep(list(list()),cycles) +T19_4_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_1_1000[[r]]) + T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_1001_2000[[r]]) + T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_2001_3000[[r]]) + T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_3001_4000[[r]]) + T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_4001_5000[[r]]) + T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_5001_6000[[r]]) + T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_6001_7000[[r]]) + T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_7001_8000[[r]]) + T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_8001_9000[[r]]) + T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_9001_10000[[r]]) + T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_10001_11000[[r]]) + T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_11001_12419[[r]]) + + T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_1_1000[[r]]) + T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_1001_2000[[r]]) + T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_2001_3000[[r]]) + T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_3001_4000[[r]]) + T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_4001_5000[[r]]) + T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_5001_6000[[r]]) + T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_6001_7000[[r]]) + T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_7001_8000[[r]]) + T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_8001_9000[[r]]) + T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_9001_10000[[r]]) + T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_10001_11000[[r]]) + T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T19_4_gfblup_prediction_all,"T19_4_gfblup_prediction_all.rds") +saveRDS(T19_4_gfblup_variances_all,"T19_4_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_5_gblup_prediction_all_1_1000=readRDS(file="T19_5_gblup_prediction_all_1_1000.rds") +T19_5_gblup_prediction_all_1001_2000=readRDS(file="T19_5_gblup_prediction_all_1001_2000.rds") +T19_5_gblup_prediction_all_2001_3000=readRDS(file="T19_5_gblup_prediction_all_2001_3000.rds") +T19_5_gblup_prediction_all_3001_4000=readRDS(file="T19_5_gblup_prediction_all_3001_4000.rds") +T19_5_gblup_prediction_all_4001_5000=readRDS(file="T19_5_gblup_prediction_all_4001_5000.rds") +T19_5_gblup_prediction_all_5001_6000=readRDS(file="T19_5_gblup_prediction_all_5001_6000.rds") +T19_5_gblup_prediction_all_6001_7000=readRDS(file="T19_5_gblup_prediction_all_6001_7000.rds") +T19_5_gblup_prediction_all_7001_8000=readRDS(file="T19_5_gblup_prediction_all_7001_8000.rds") +T19_5_gblup_prediction_all_8001_9000=readRDS(file="T19_5_gblup_prediction_all_8001_9000.rds") +T19_5_gblup_prediction_all_9001_10000=readRDS(file="T19_5_gblup_prediction_all_9001_10000.rds") +T19_5_gblup_prediction_all_10001_11000=readRDS(file="T19_5_gblup_prediction_all_10001_11000.rds") +T19_5_gblup_prediction_all_11001_12419=readRDS(file="T19_5_gblup_prediction_all_11001_12419.rds") +T19_5_gblup_prediction_all=c(T19_5_gblup_prediction_all_1_1000,T19_5_gblup_prediction_all_1001_2000,T19_5_gblup_prediction_all_2001_3000,T19_5_gblup_prediction_all_3001_4000,T19_5_gblup_prediction_all_4001_5000,T19_5_gblup_prediction_all_5001_6000,T19_5_gblup_prediction_all_6001_7000,T19_5_gblup_prediction_all_7001_8000,T19_5_gblup_prediction_all_8001_9000,T19_5_gblup_prediction_all_9001_10000,T19_5_gblup_prediction_all_10001_11000,T19_5_gblup_prediction_all_11001_12419) + +T19_5_gblup_variances_all_1_1000=readRDS(file="T19_5_gblup_variances_all_1_1000.rds") +T19_5_gblup_variances_all_1001_2000=readRDS(file="T19_5_gblup_variances_all_1001_2000.rds") +T19_5_gblup_variances_all_2001_3000=readRDS(file="T19_5_gblup_variances_all_2001_3000.rds") +T19_5_gblup_variances_all_3001_4000=readRDS(file="T19_5_gblup_variances_all_3001_4000.rds") +T19_5_gblup_variances_all_4001_5000=readRDS(file="T19_5_gblup_variances_all_4001_5000.rds") +T19_5_gblup_variances_all_5001_6000=readRDS(file="T19_5_gblup_variances_all_5001_6000.rds") +T19_5_gblup_variances_all_6001_7000=readRDS(file="T19_5_gblup_variances_all_6001_7000.rds") +T19_5_gblup_variances_all_7001_8000=readRDS(file="T19_5_gblup_variances_all_7001_8000.rds") +T19_5_gblup_variances_all_8001_9000=readRDS(file="T19_5_gblup_variances_all_8001_9000.rds") +T19_5_gblup_variances_all_9001_10000=readRDS(file="T19_5_gblup_variances_all_9001_10000.rds") +T19_5_gblup_variances_all_10001_11000=readRDS(file="T19_5_gblup_variances_all_10001_11000.rds") +T19_5_gblup_variances_all_11001_12419=readRDS(file="T19_5_gblup_variances_all_11001_12419.rds") +T19_5_gblup_variances_all=c(T19_5_gblup_variances_all_1_1000,T19_5_gblup_variances_all_1001_2000,T19_5_gblup_variances_all_2001_3000,T19_5_gblup_variances_all_3001_4000,T19_5_gblup_variances_all_4001_5000,T19_5_gblup_variances_all_5001_6000,T19_5_gblup_variances_all_6001_7000,T19_5_gblup_variances_all_7001_8000,T19_5_gblup_variances_all_8001_9000,T19_5_gblup_variances_all_9001_10000,T19_5_gblup_variances_all_10001_11000,T19_5_gblup_variances_all_11001_12419) + +saveRDS(T19_5_gblup_prediction_all,"T19_5_gblup_prediction_all.rds") +saveRDS(T19_5_gblup_variances_all,"T19_5_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_5_gfblup_prediction_all_1_1000=readRDS(file="T19_5_gfblup_prediction_all_1_1000.rds") +T19_5_gfblup_prediction_all_1001_2000=readRDS(file="T19_5_gfblup_prediction_all_1001_2000.rds") +T19_5_gfblup_prediction_all_2001_3000=readRDS(file="T19_5_gfblup_prediction_all_2001_3000.rds") +T19_5_gfblup_prediction_all_3001_4000=readRDS(file="T19_5_gfblup_prediction_all_3001_4000.rds") +T19_5_gfblup_prediction_all_4001_5000=readRDS(file="T19_5_gfblup_prediction_all_4001_5000.rds") +T19_5_gfblup_prediction_all_5001_6000=readRDS(file="T19_5_gfblup_prediction_all_5001_6000.rds") +T19_5_gfblup_prediction_all_6001_7000=readRDS(file="T19_5_gfblup_prediction_all_6001_7000.rds") +T19_5_gfblup_prediction_all_7001_8000=readRDS(file="T19_5_gfblup_prediction_all_7001_8000.rds") +T19_5_gfblup_prediction_all_8001_9000=readRDS(file="T19_5_gfblup_prediction_all_8001_9000.rds") +T19_5_gfblup_prediction_all_9001_10000=readRDS(file="T19_5_gfblup_prediction_all_9001_10000.rds") +T19_5_gfblup_prediction_all_10001_11000=readRDS(file="T19_5_gfblup_prediction_all_10001_11000.rds") +T19_5_gfblup_prediction_all_11001_12419=readRDS(file="T19_5_gfblup_prediction_all_11001_12419.rds") + +T19_5_gfblup_variances_all_1_1000=readRDS(file="T19_5_gfblup_variances_all_1_1000.rds") +T19_5_gfblup_variances_all_1001_2000=readRDS(file="T19_5_gfblup_variances_all_1001_2000.rds") +T19_5_gfblup_variances_all_2001_3000=readRDS(file="T19_5_gfblup_variances_all_2001_3000.rds") +T19_5_gfblup_variances_all_3001_4000=readRDS(file="T19_5_gfblup_variances_all_3001_4000.rds") +T19_5_gfblup_variances_all_4001_5000=readRDS(file="T19_5_gfblup_variances_all_4001_5000.rds") +T19_5_gfblup_variances_all_5001_6000=readRDS(file="T19_5_gfblup_variances_all_5001_6000.rds") +T19_5_gfblup_variances_all_6001_7000=readRDS(file="T19_5_gfblup_variances_all_6001_7000.rds") +T19_5_gfblup_variances_all_7001_8000=readRDS(file="T19_5_gfblup_variances_all_7001_8000.rds") +T19_5_gfblup_variances_all_8001_9000=readRDS(file="T19_5_gfblup_variances_all_8001_9000.rds") +T19_5_gfblup_variances_all_9001_10000=readRDS(file="T19_5_gfblup_variances_all_9001_10000.rds") +T19_5_gfblup_variances_all_10001_11000=readRDS(file="T19_5_gfblup_variances_all_10001_11000.rds") +T19_5_gfblup_variances_all_11001_12419=readRDS(file="T19_5_gfblup_variances_all_11001_12419.rds") + +cycles=length(T19_5_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T19_5_gfblup_variances_all=rep(list(list()),cycles) +T19_5_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_1_1000[[r]]) + T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_1001_2000[[r]]) + T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_2001_3000[[r]]) + T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_3001_4000[[r]]) + T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_4001_5000[[r]]) + T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_5001_6000[[r]]) + T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_6001_7000[[r]]) + T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_7001_8000[[r]]) + T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_8001_9000[[r]]) + T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_9001_10000[[r]]) + T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_10001_11000[[r]]) + T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_11001_12419[[r]]) + + T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_1_1000[[r]]) + T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_1001_2000[[r]]) + T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_2001_3000[[r]]) + T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_3001_4000[[r]]) + T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_4001_5000[[r]]) + T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_5001_6000[[r]]) + T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_6001_7000[[r]]) + T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_7001_8000[[r]]) + T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_8001_9000[[r]]) + T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_9001_10000[[r]]) + T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_10001_11000[[r]]) + T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T19_5_gfblup_prediction_all,"T19_5_gfblup_prediction_all.rds") +saveRDS(T19_5_gfblup_variances_all,"T19_5_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_6_gblup_prediction_all_1_1000=readRDS(file="T19_6_gblup_prediction_all_1_1000.rds") +T19_6_gblup_prediction_all_1001_2000=readRDS(file="T19_6_gblup_prediction_all_1001_2000.rds") +T19_6_gblup_prediction_all_2001_3000=readRDS(file="T19_6_gblup_prediction_all_2001_3000.rds") +T19_6_gblup_prediction_all_3001_4000=readRDS(file="T19_6_gblup_prediction_all_3001_4000.rds") +T19_6_gblup_prediction_all_4001_5000=readRDS(file="T19_6_gblup_prediction_all_4001_5000.rds") +T19_6_gblup_prediction_all_5001_6000=readRDS(file="T19_6_gblup_prediction_all_5001_6000.rds") +T19_6_gblup_prediction_all_6001_7000=readRDS(file="T19_6_gblup_prediction_all_6001_7000.rds") +T19_6_gblup_prediction_all_7001_8000=readRDS(file="T19_6_gblup_prediction_all_7001_8000.rds") +T19_6_gblup_prediction_all_8001_9000=readRDS(file="T19_6_gblup_prediction_all_8001_9000.rds") +T19_6_gblup_prediction_all_9001_10000=readRDS(file="T19_6_gblup_prediction_all_9001_10000.rds") +T19_6_gblup_prediction_all_10001_11000=readRDS(file="T19_6_gblup_prediction_all_10001_11000.rds") +T19_6_gblup_prediction_all_11001_12419=readRDS(file="T19_6_gblup_prediction_all_11001_12419.rds") +T19_6_gblup_prediction_all=c(T19_6_gblup_prediction_all_1_1000,T19_6_gblup_prediction_all_1001_2000,T19_6_gblup_prediction_all_2001_3000,T19_6_gblup_prediction_all_3001_4000,T19_6_gblup_prediction_all_4001_5000,T19_6_gblup_prediction_all_5001_6000,T19_6_gblup_prediction_all_6001_7000,T19_6_gblup_prediction_all_7001_8000,T19_6_gblup_prediction_all_8001_9000,T19_6_gblup_prediction_all_9001_10000,T19_6_gblup_prediction_all_10001_11000,T19_6_gblup_prediction_all_11001_12419) + +T19_6_gblup_variances_all_1_1000=readRDS(file="T19_6_gblup_variances_all_1_1000.rds") +T19_6_gblup_variances_all_1001_2000=readRDS(file="T19_6_gblup_variances_all_1001_2000.rds") +T19_6_gblup_variances_all_2001_3000=readRDS(file="T19_6_gblup_variances_all_2001_3000.rds") +T19_6_gblup_variances_all_3001_4000=readRDS(file="T19_6_gblup_variances_all_3001_4000.rds") +T19_6_gblup_variances_all_4001_5000=readRDS(file="T19_6_gblup_variances_all_4001_5000.rds") +T19_6_gblup_variances_all_5001_6000=readRDS(file="T19_6_gblup_variances_all_5001_6000.rds") +T19_6_gblup_variances_all_6001_7000=readRDS(file="T19_6_gblup_variances_all_6001_7000.rds") +T19_6_gblup_variances_all_7001_8000=readRDS(file="T19_6_gblup_variances_all_7001_8000.rds") +T19_6_gblup_variances_all_8001_9000=readRDS(file="T19_6_gblup_variances_all_8001_9000.rds") +T19_6_gblup_variances_all_9001_10000=readRDS(file="T19_6_gblup_variances_all_9001_10000.rds") +T19_6_gblup_variances_all_10001_11000=readRDS(file="T19_6_gblup_variances_all_10001_11000.rds") +T19_6_gblup_variances_all_11001_12419=readRDS(file="T19_6_gblup_variances_all_11001_12419.rds") +T19_6_gblup_variances_all=c(T19_6_gblup_variances_all_1_1000,T19_6_gblup_variances_all_1001_2000,T19_6_gblup_variances_all_2001_3000,T19_6_gblup_variances_all_3001_4000,T19_6_gblup_variances_all_4001_5000,T19_6_gblup_variances_all_5001_6000,T19_6_gblup_variances_all_6001_7000,T19_6_gblup_variances_all_7001_8000,T19_6_gblup_variances_all_8001_9000,T19_6_gblup_variances_all_9001_10000,T19_6_gblup_variances_all_10001_11000,T19_6_gblup_variances_all_11001_12419) + +saveRDS(T19_6_gblup_prediction_all,"T19_6_gblup_prediction_all.rds") +saveRDS(T19_6_gblup_variances_all,"T19_6_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_6_gfblup_prediction_all_1_1000=readRDS(file="T19_6_gfblup_prediction_all_1_1000.rds") +T19_6_gfblup_prediction_all_1001_2000=readRDS(file="T19_6_gfblup_prediction_all_1001_2000.rds") +T19_6_gfblup_prediction_all_2001_3000=readRDS(file="T19_6_gfblup_prediction_all_2001_3000.rds") +T19_6_gfblup_prediction_all_3001_4000=readRDS(file="T19_6_gfblup_prediction_all_3001_4000.rds") +T19_6_gfblup_prediction_all_4001_5000=readRDS(file="T19_6_gfblup_prediction_all_4001_5000.rds") +T19_6_gfblup_prediction_all_5001_6000=readRDS(file="T19_6_gfblup_prediction_all_5001_6000.rds") +T19_6_gfblup_prediction_all_6001_7000=readRDS(file="T19_6_gfblup_prediction_all_6001_7000.rds") +T19_6_gfblup_prediction_all_7001_8000=readRDS(file="T19_6_gfblup_prediction_all_7001_8000.rds") +T19_6_gfblup_prediction_all_8001_9000=readRDS(file="T19_6_gfblup_prediction_all_8001_9000.rds") +T19_6_gfblup_prediction_all_9001_10000=readRDS(file="T19_6_gfblup_prediction_all_9001_10000.rds") +T19_6_gfblup_prediction_all_10001_11000=readRDS(file="T19_6_gfblup_prediction_all_10001_11000.rds") +T19_6_gfblup_prediction_all_11001_12419=readRDS(file="T19_6_gfblup_prediction_all_11001_12419.rds") + +T19_6_gfblup_variances_all_1_1000=readRDS(file="T19_6_gfblup_variances_all_1_1000.rds") +T19_6_gfblup_variances_all_1001_2000=readRDS(file="T19_6_gfblup_variances_all_1001_2000.rds") +T19_6_gfblup_variances_all_2001_3000=readRDS(file="T19_6_gfblup_variances_all_2001_3000.rds") +T19_6_gfblup_variances_all_3001_4000=readRDS(file="T19_6_gfblup_variances_all_3001_4000.rds") +T19_6_gfblup_variances_all_4001_5000=readRDS(file="T19_6_gfblup_variances_all_4001_5000.rds") +T19_6_gfblup_variances_all_5001_6000=readRDS(file="T19_6_gfblup_variances_all_5001_6000.rds") +T19_6_gfblup_variances_all_6001_7000=readRDS(file="T19_6_gfblup_variances_all_6001_7000.rds") +T19_6_gfblup_variances_all_7001_8000=readRDS(file="T19_6_gfblup_variances_all_7001_8000.rds") +T19_6_gfblup_variances_all_8001_9000=readRDS(file="T19_6_gfblup_variances_all_8001_9000.rds") +T19_6_gfblup_variances_all_9001_10000=readRDS(file="T19_6_gfblup_variances_all_9001_10000.rds") +T19_6_gfblup_variances_all_10001_11000=readRDS(file="T19_6_gfblup_variances_all_10001_11000.rds") +T19_6_gfblup_variances_all_11001_12419=readRDS(file="T19_6_gfblup_variances_all_11001_12419.rds") + +cycles=length(T19_6_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T19_6_gfblup_variances_all=rep(list(list()),cycles) +T19_6_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_1_1000[[r]]) + T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_1001_2000[[r]]) + T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_2001_3000[[r]]) + T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_3001_4000[[r]]) + T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_4001_5000[[r]]) + T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_5001_6000[[r]]) + T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_6001_7000[[r]]) + T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_7001_8000[[r]]) + T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_8001_9000[[r]]) + T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_9001_10000[[r]]) + T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_10001_11000[[r]]) + T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_11001_12419[[r]]) + + T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_1_1000[[r]]) + T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_1001_2000[[r]]) + T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_2001_3000[[r]]) + T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_3001_4000[[r]]) + T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_4001_5000[[r]]) + T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_5001_6000[[r]]) + T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_6001_7000[[r]]) + T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_7001_8000[[r]]) + T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_8001_9000[[r]]) + T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_9001_10000[[r]]) + T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_10001_11000[[r]]) + T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T19_6_gfblup_prediction_all,"T19_6_gfblup_prediction_all.rds") +saveRDS(T19_6_gfblup_variances_all,"T19_6_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_7_gblup_prediction_all_1_1000=readRDS(file="T19_7_gblup_prediction_all_1_1000.rds") +T19_7_gblup_prediction_all_1001_2000=readRDS(file="T19_7_gblup_prediction_all_1001_2000.rds") +T19_7_gblup_prediction_all_2001_3000=readRDS(file="T19_7_gblup_prediction_all_2001_3000.rds") +T19_7_gblup_prediction_all_3001_4000=readRDS(file="T19_7_gblup_prediction_all_3001_4000.rds") +T19_7_gblup_prediction_all_4001_5000=readRDS(file="T19_7_gblup_prediction_all_4001_5000.rds") +T19_7_gblup_prediction_all_5001_6000=readRDS(file="T19_7_gblup_prediction_all_5001_6000.rds") +T19_7_gblup_prediction_all_6001_7000=readRDS(file="T19_7_gblup_prediction_all_6001_7000.rds") +T19_7_gblup_prediction_all_7001_8000=readRDS(file="T19_7_gblup_prediction_all_7001_8000.rds") +T19_7_gblup_prediction_all_8001_9000=readRDS(file="T19_7_gblup_prediction_all_8001_9000.rds") +T19_7_gblup_prediction_all_9001_10000=readRDS(file="T19_7_gblup_prediction_all_9001_10000.rds") +T19_7_gblup_prediction_all_10001_11000=readRDS(file="T19_7_gblup_prediction_all_10001_11000.rds") +T19_7_gblup_prediction_all_11001_12419=readRDS(file="T19_7_gblup_prediction_all_11001_12419.rds") +T19_7_gblup_prediction_all=c(T19_7_gblup_prediction_all_1_1000,T19_7_gblup_prediction_all_1001_2000,T19_7_gblup_prediction_all_2001_3000,T19_7_gblup_prediction_all_3001_4000,T19_7_gblup_prediction_all_4001_5000,T19_7_gblup_prediction_all_5001_6000,T19_7_gblup_prediction_all_6001_7000,T19_7_gblup_prediction_all_7001_8000,T19_7_gblup_prediction_all_8001_9000,T19_7_gblup_prediction_all_9001_10000,T19_7_gblup_prediction_all_10001_11000,T19_7_gblup_prediction_all_11001_12419) + +T19_7_gblup_variances_all_1_1000=readRDS(file="T19_7_gblup_variances_all_1_1000.rds") +T19_7_gblup_variances_all_1001_2000=readRDS(file="T19_7_gblup_variances_all_1001_2000.rds") +T19_7_gblup_variances_all_2001_3000=readRDS(file="T19_7_gblup_variances_all_2001_3000.rds") +T19_7_gblup_variances_all_3001_4000=readRDS(file="T19_7_gblup_variances_all_3001_4000.rds") +T19_7_gblup_variances_all_4001_5000=readRDS(file="T19_7_gblup_variances_all_4001_5000.rds") +T19_7_gblup_variances_all_5001_6000=readRDS(file="T19_7_gblup_variances_all_5001_6000.rds") +T19_7_gblup_variances_all_6001_7000=readRDS(file="T19_7_gblup_variances_all_6001_7000.rds") +T19_7_gblup_variances_all_7001_8000=readRDS(file="T19_7_gblup_variances_all_7001_8000.rds") +T19_7_gblup_variances_all_8001_9000=readRDS(file="T19_7_gblup_variances_all_8001_9000.rds") +T19_7_gblup_variances_all_9001_10000=readRDS(file="T19_7_gblup_variances_all_9001_10000.rds") +T19_7_gblup_variances_all_10001_11000=readRDS(file="T19_7_gblup_variances_all_10001_11000.rds") +T19_7_gblup_variances_all_11001_12419=readRDS(file="T19_7_gblup_variances_all_11001_12419.rds") +T19_7_gblup_variances_all=c(T19_7_gblup_variances_all_1_1000,T19_7_gblup_variances_all_1001_2000,T19_7_gblup_variances_all_2001_3000,T19_7_gblup_variances_all_3001_4000,T19_7_gblup_variances_all_4001_5000,T19_7_gblup_variances_all_5001_6000,T19_7_gblup_variances_all_6001_7000,T19_7_gblup_variances_all_7001_8000,T19_7_gblup_variances_all_8001_9000,T19_7_gblup_variances_all_9001_10000,T19_7_gblup_variances_all_10001_11000,T19_7_gblup_variances_all_11001_12419) + +saveRDS(T19_7_gblup_prediction_all,"T19_7_gblup_prediction_all.rds") +saveRDS(T19_7_gblup_variances_all,"T19_7_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_7_gfblup_prediction_all_1_1000=readRDS(file="T19_7_gfblup_prediction_all_1_1000.rds") +T19_7_gfblup_prediction_all_1001_2000=readRDS(file="T19_7_gfblup_prediction_all_1001_2000.rds") +T19_7_gfblup_prediction_all_2001_3000=readRDS(file="T19_7_gfblup_prediction_all_2001_3000.rds") +T19_7_gfblup_prediction_all_3001_4000=readRDS(file="T19_7_gfblup_prediction_all_3001_4000.rds") +T19_7_gfblup_prediction_all_4001_5000=readRDS(file="T19_7_gfblup_prediction_all_4001_5000.rds") +T19_7_gfblup_prediction_all_5001_6000=readRDS(file="T19_7_gfblup_prediction_all_5001_6000.rds") +T19_7_gfblup_prediction_all_6001_7000=readRDS(file="T19_7_gfblup_prediction_all_6001_7000.rds") +T19_7_gfblup_prediction_all_7001_8000=readRDS(file="T19_7_gfblup_prediction_all_7001_8000.rds") +T19_7_gfblup_prediction_all_8001_9000=readRDS(file="T19_7_gfblup_prediction_all_8001_9000.rds") +T19_7_gfblup_prediction_all_9001_10000=readRDS(file="T19_7_gfblup_prediction_all_9001_10000.rds") +T19_7_gfblup_prediction_all_10001_11000=readRDS(file="T19_7_gfblup_prediction_all_10001_11000.rds") +T19_7_gfblup_prediction_all_11001_12419=readRDS(file="T19_7_gfblup_prediction_all_11001_12419.rds") + +T19_7_gfblup_variances_all_1_1000=readRDS(file="T19_7_gfblup_variances_all_1_1000.rds") +T19_7_gfblup_variances_all_1001_2000=readRDS(file="T19_7_gfblup_variances_all_1001_2000.rds") +T19_7_gfblup_variances_all_2001_3000=readRDS(file="T19_7_gfblup_variances_all_2001_3000.rds") +T19_7_gfblup_variances_all_3001_4000=readRDS(file="T19_7_gfblup_variances_all_3001_4000.rds") +T19_7_gfblup_variances_all_4001_5000=readRDS(file="T19_7_gfblup_variances_all_4001_5000.rds") +T19_7_gfblup_variances_all_5001_6000=readRDS(file="T19_7_gfblup_variances_all_5001_6000.rds") +T19_7_gfblup_variances_all_6001_7000=readRDS(file="T19_7_gfblup_variances_all_6001_7000.rds") +T19_7_gfblup_variances_all_7001_8000=readRDS(file="T19_7_gfblup_variances_all_7001_8000.rds") +T19_7_gfblup_variances_all_8001_9000=readRDS(file="T19_7_gfblup_variances_all_8001_9000.rds") +T19_7_gfblup_variances_all_9001_10000=readRDS(file="T19_7_gfblup_variances_all_9001_10000.rds") +T19_7_gfblup_variances_all_10001_11000=readRDS(file="T19_7_gfblup_variances_all_10001_11000.rds") +T19_7_gfblup_variances_all_11001_12419=readRDS(file="T19_7_gfblup_variances_all_11001_12419.rds") + +cycles=length(T19_7_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T19_7_gfblup_variances_all=rep(list(list()),cycles) +T19_7_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_1_1000[[r]]) + T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_1001_2000[[r]]) + T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_2001_3000[[r]]) + T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_3001_4000[[r]]) + T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_4001_5000[[r]]) + T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_5001_6000[[r]]) + T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_6001_7000[[r]]) + T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_7001_8000[[r]]) + T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_8001_9000[[r]]) + T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_9001_10000[[r]]) + T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_10001_11000[[r]]) + T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_11001_12419[[r]]) + + T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_1_1000[[r]]) + T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_1001_2000[[r]]) + T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_2001_3000[[r]]) + T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_3001_4000[[r]]) + T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_4001_5000[[r]]) + T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_5001_6000[[r]]) + T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_6001_7000[[r]]) + T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_7001_8000[[r]]) + T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_8001_9000[[r]]) + T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_9001_10000[[r]]) + T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_10001_11000[[r]]) + T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T19_7_gfblup_prediction_all,"T19_7_gfblup_prediction_all.rds") +saveRDS(T19_7_gfblup_variances_all,"T19_7_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_8_gblup_prediction_all_1_1000=readRDS(file="T19_8_gblup_prediction_all_1_1000.rds") +T19_8_gblup_prediction_all_1001_2000=readRDS(file="T19_8_gblup_prediction_all_1001_2000.rds") +T19_8_gblup_prediction_all_2001_3000=readRDS(file="T19_8_gblup_prediction_all_2001_3000.rds") +T19_8_gblup_prediction_all_3001_4000=readRDS(file="T19_8_gblup_prediction_all_3001_4000.rds") +T19_8_gblup_prediction_all_4001_5000=readRDS(file="T19_8_gblup_prediction_all_4001_5000.rds") +T19_8_gblup_prediction_all_5001_6000=readRDS(file="T19_8_gblup_prediction_all_5001_6000.rds") +T19_8_gblup_prediction_all_6001_7000=readRDS(file="T19_8_gblup_prediction_all_6001_7000.rds") +T19_8_gblup_prediction_all_7001_8000=readRDS(file="T19_8_gblup_prediction_all_7001_8000.rds") +T19_8_gblup_prediction_all_8001_9000=readRDS(file="T19_8_gblup_prediction_all_8001_9000.rds") +T19_8_gblup_prediction_all_9001_10000=readRDS(file="T19_8_gblup_prediction_all_9001_10000.rds") +T19_8_gblup_prediction_all_10001_11000=readRDS(file="T19_8_gblup_prediction_all_10001_11000.rds") +T19_8_gblup_prediction_all_11001_12419=readRDS(file="T19_8_gblup_prediction_all_11001_12419.rds") +T19_8_gblup_prediction_all=c(T19_8_gblup_prediction_all_1_1000,T19_8_gblup_prediction_all_1001_2000,T19_8_gblup_prediction_all_2001_3000,T19_8_gblup_prediction_all_3001_4000,T19_8_gblup_prediction_all_4001_5000,T19_8_gblup_prediction_all_5001_6000,T19_8_gblup_prediction_all_6001_7000,T19_8_gblup_prediction_all_7001_8000,T19_8_gblup_prediction_all_8001_9000,T19_8_gblup_prediction_all_9001_10000,T19_8_gblup_prediction_all_10001_11000,T19_8_gblup_prediction_all_11001_12419) + +T19_8_gblup_variances_all_1_1000=readRDS(file="T19_8_gblup_variances_all_1_1000.rds") +T19_8_gblup_variances_all_1001_2000=readRDS(file="T19_8_gblup_variances_all_1001_2000.rds") +T19_8_gblup_variances_all_2001_3000=readRDS(file="T19_8_gblup_variances_all_2001_3000.rds") +T19_8_gblup_variances_all_3001_4000=readRDS(file="T19_8_gblup_variances_all_3001_4000.rds") +T19_8_gblup_variances_all_4001_5000=readRDS(file="T19_8_gblup_variances_all_4001_5000.rds") +T19_8_gblup_variances_all_5001_6000=readRDS(file="T19_8_gblup_variances_all_5001_6000.rds") +T19_8_gblup_variances_all_6001_7000=readRDS(file="T19_8_gblup_variances_all_6001_7000.rds") +T19_8_gblup_variances_all_7001_8000=readRDS(file="T19_8_gblup_variances_all_7001_8000.rds") +T19_8_gblup_variances_all_8001_9000=readRDS(file="T19_8_gblup_variances_all_8001_9000.rds") +T19_8_gblup_variances_all_9001_10000=readRDS(file="T19_8_gblup_variances_all_9001_10000.rds") +T19_8_gblup_variances_all_10001_11000=readRDS(file="T19_8_gblup_variances_all_10001_11000.rds") +T19_8_gblup_variances_all_11001_12419=readRDS(file="T19_8_gblup_variances_all_11001_12419.rds") +T19_8_gblup_variances_all=c(T19_8_gblup_variances_all_1_1000,T19_8_gblup_variances_all_1001_2000,T19_8_gblup_variances_all_2001_3000,T19_8_gblup_variances_all_3001_4000,T19_8_gblup_variances_all_4001_5000,T19_8_gblup_variances_all_5001_6000,T19_8_gblup_variances_all_6001_7000,T19_8_gblup_variances_all_7001_8000,T19_8_gblup_variances_all_8001_9000,T19_8_gblup_variances_all_9001_10000,T19_8_gblup_variances_all_10001_11000,T19_8_gblup_variances_all_11001_12419) + +saveRDS(T19_8_gblup_prediction_all,"T19_8_gblup_prediction_all.rds") +saveRDS(T19_8_gblup_variances_all,"T19_8_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_8_gfblup_prediction_all_1_1000=readRDS(file="T19_8_gfblup_prediction_all_1_1000.rds") +T19_8_gfblup_prediction_all_1001_2000=readRDS(file="T19_8_gfblup_prediction_all_1001_2000.rds") +T19_8_gfblup_prediction_all_2001_3000=readRDS(file="T19_8_gfblup_prediction_all_2001_3000.rds") +T19_8_gfblup_prediction_all_3001_4000=readRDS(file="T19_8_gfblup_prediction_all_3001_4000.rds") +T19_8_gfblup_prediction_all_4001_5000=readRDS(file="T19_8_gfblup_prediction_all_4001_5000.rds") +T19_8_gfblup_prediction_all_5001_6000=readRDS(file="T19_8_gfblup_prediction_all_5001_6000.rds") +T19_8_gfblup_prediction_all_6001_7000=readRDS(file="T19_8_gfblup_prediction_all_6001_7000.rds") +T19_8_gfblup_prediction_all_7001_8000=readRDS(file="T19_8_gfblup_prediction_all_7001_8000.rds") +T19_8_gfblup_prediction_all_8001_9000=readRDS(file="T19_8_gfblup_prediction_all_8001_9000.rds") +T19_8_gfblup_prediction_all_9001_10000=readRDS(file="T19_8_gfblup_prediction_all_9001_10000.rds") +T19_8_gfblup_prediction_all_10001_11000=readRDS(file="T19_8_gfblup_prediction_all_10001_11000.rds") +T19_8_gfblup_prediction_all_11001_12419=readRDS(file="T19_8_gfblup_prediction_all_11001_12419.rds") + +T19_8_gfblup_variances_all_1_1000=readRDS(file="T19_8_gfblup_variances_all_1_1000.rds") +T19_8_gfblup_variances_all_1001_2000=readRDS(file="T19_8_gfblup_variances_all_1001_2000.rds") +T19_8_gfblup_variances_all_2001_3000=readRDS(file="T19_8_gfblup_variances_all_2001_3000.rds") +T19_8_gfblup_variances_all_3001_4000=readRDS(file="T19_8_gfblup_variances_all_3001_4000.rds") +T19_8_gfblup_variances_all_4001_5000=readRDS(file="T19_8_gfblup_variances_all_4001_5000.rds") +T19_8_gfblup_variances_all_5001_6000=readRDS(file="T19_8_gfblup_variances_all_5001_6000.rds") +T19_8_gfblup_variances_all_6001_7000=readRDS(file="T19_8_gfblup_variances_all_6001_7000.rds") +T19_8_gfblup_variances_all_7001_8000=readRDS(file="T19_8_gfblup_variances_all_7001_8000.rds") +T19_8_gfblup_variances_all_8001_9000=readRDS(file="T19_8_gfblup_variances_all_8001_9000.rds") +T19_8_gfblup_variances_all_9001_10000=readRDS(file="T19_8_gfblup_variances_all_9001_10000.rds") +T19_8_gfblup_variances_all_10001_11000=readRDS(file="T19_8_gfblup_variances_all_10001_11000.rds") +T19_8_gfblup_variances_all_11001_12419=readRDS(file="T19_8_gfblup_variances_all_11001_12419.rds") + +cycles=length(T19_8_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T19_8_gfblup_variances_all=rep(list(list()),cycles) +T19_8_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_1_1000[[r]]) + T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_1001_2000[[r]]) + T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_2001_3000[[r]]) + T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_3001_4000[[r]]) + T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_4001_5000[[r]]) + T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_5001_6000[[r]]) + T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_6001_7000[[r]]) + T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_7001_8000[[r]]) + T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_8001_9000[[r]]) + T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_9001_10000[[r]]) + T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_10001_11000[[r]]) + T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_11001_12419[[r]]) + + T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_1_1000[[r]]) + T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_1001_2000[[r]]) + T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_2001_3000[[r]]) + T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_3001_4000[[r]]) + T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_4001_5000[[r]]) + T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_5001_6000[[r]]) + T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_6001_7000[[r]]) + T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_7001_8000[[r]]) + T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_8001_9000[[r]]) + T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_9001_10000[[r]]) + T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_10001_11000[[r]]) + T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T19_8_gfblup_prediction_all,"T19_8_gfblup_prediction_all.rds") +saveRDS(T19_8_gfblup_variances_all,"T19_8_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T20_1_gblup_prediction_all_1_1000=readRDS(file="T20_1_gblup_prediction_all_1_1000.rds") +T20_1_gblup_prediction_all_1001_2000=readRDS(file="T20_1_gblup_prediction_all_1001_2000.rds") +T20_1_gblup_prediction_all_2001_3000=readRDS(file="T20_1_gblup_prediction_all_2001_3000.rds") +T20_1_gblup_prediction_all_3001_4000=readRDS(file="T20_1_gblup_prediction_all_3001_4000.rds") +T20_1_gblup_prediction_all_4001_5000=readRDS(file="T20_1_gblup_prediction_all_4001_5000.rds") +T20_1_gblup_prediction_all_5001_6000=readRDS(file="T20_1_gblup_prediction_all_5001_6000.rds") +T20_1_gblup_prediction_all_6001_7000=readRDS(file="T20_1_gblup_prediction_all_6001_7000.rds") +T20_1_gblup_prediction_all_7001_8000=readRDS(file="T20_1_gblup_prediction_all_7001_8000.rds") +T20_1_gblup_prediction_all_8001_9000=readRDS(file="T20_1_gblup_prediction_all_8001_9000.rds") +T20_1_gblup_prediction_all_9001_10000=readRDS(file="T20_1_gblup_prediction_all_9001_10000.rds") +T20_1_gblup_prediction_all_10001_11000=readRDS(file="T20_1_gblup_prediction_all_10001_11000.rds") +T20_1_gblup_prediction_all_11001_12419=readRDS(file="T20_1_gblup_prediction_all_11001_12419.rds") +T20_1_gblup_prediction_all=c(T20_1_gblup_prediction_all_1_1000,T20_1_gblup_prediction_all_1001_2000,T20_1_gblup_prediction_all_2001_3000,T20_1_gblup_prediction_all_3001_4000,T20_1_gblup_prediction_all_4001_5000,T20_1_gblup_prediction_all_5001_6000,T20_1_gblup_prediction_all_6001_7000,T20_1_gblup_prediction_all_7001_8000,T20_1_gblup_prediction_all_8001_9000,T20_1_gblup_prediction_all_9001_10000,T20_1_gblup_prediction_all_10001_11000,T20_1_gblup_prediction_all_11001_12419) + +T20_1_gblup_variances_all_1_1000=readRDS(file="T20_1_gblup_variances_all_1_1000.rds") +T20_1_gblup_variances_all_1001_2000=readRDS(file="T20_1_gblup_variances_all_1001_2000.rds") +T20_1_gblup_variances_all_2001_3000=readRDS(file="T20_1_gblup_variances_all_2001_3000.rds") +T20_1_gblup_variances_all_3001_4000=readRDS(file="T20_1_gblup_variances_all_3001_4000.rds") +T20_1_gblup_variances_all_4001_5000=readRDS(file="T20_1_gblup_variances_all_4001_5000.rds") +T20_1_gblup_variances_all_5001_6000=readRDS(file="T20_1_gblup_variances_all_5001_6000.rds") +T20_1_gblup_variances_all_6001_7000=readRDS(file="T20_1_gblup_variances_all_6001_7000.rds") +T20_1_gblup_variances_all_7001_8000=readRDS(file="T20_1_gblup_variances_all_7001_8000.rds") +T20_1_gblup_variances_all_8001_9000=readRDS(file="T20_1_gblup_variances_all_8001_9000.rds") +T20_1_gblup_variances_all_9001_10000=readRDS(file="T20_1_gblup_variances_all_9001_10000.rds") +T20_1_gblup_variances_all_10001_11000=readRDS(file="T20_1_gblup_variances_all_10001_11000.rds") +T20_1_gblup_variances_all_11001_12419=readRDS(file="T20_1_gblup_variances_all_11001_12419.rds") +T20_1_gblup_variances_all=c(T20_1_gblup_variances_all_1_1000,T20_1_gblup_variances_all_1001_2000,T20_1_gblup_variances_all_2001_3000,T20_1_gblup_variances_all_3001_4000,T20_1_gblup_variances_all_4001_5000,T20_1_gblup_variances_all_5001_6000,T20_1_gblup_variances_all_6001_7000,T20_1_gblup_variances_all_7001_8000,T20_1_gblup_variances_all_8001_9000,T20_1_gblup_variances_all_9001_10000,T20_1_gblup_variances_all_10001_11000,T20_1_gblup_variances_all_11001_12419) + +saveRDS(T20_1_gblup_prediction_all,"T20_1_gblup_prediction_all.rds") +saveRDS(T20_1_gblup_variances_all,"T20_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T20_1_gfblup_prediction_all_1_1000=readRDS(file="T20_1_gfblup_prediction_all_1_1000.rds") +T20_1_gfblup_prediction_all_1001_2000=readRDS(file="T20_1_gfblup_prediction_all_1001_2000.rds") +T20_1_gfblup_prediction_all_2001_3000=readRDS(file="T20_1_gfblup_prediction_all_2001_3000.rds") +T20_1_gfblup_prediction_all_3001_4000=readRDS(file="T20_1_gfblup_prediction_all_3001_4000.rds") +T20_1_gfblup_prediction_all_4001_5000=readRDS(file="T20_1_gfblup_prediction_all_4001_5000.rds") +T20_1_gfblup_prediction_all_5001_6000=readRDS(file="T20_1_gfblup_prediction_all_5001_6000.rds") +T20_1_gfblup_prediction_all_6001_7000=readRDS(file="T20_1_gfblup_prediction_all_6001_7000.rds") +T20_1_gfblup_prediction_all_7001_8000=readRDS(file="T20_1_gfblup_prediction_all_7001_8000.rds") +T20_1_gfblup_prediction_all_8001_9000=readRDS(file="T20_1_gfblup_prediction_all_8001_9000.rds") +T20_1_gfblup_prediction_all_9001_10000=readRDS(file="T20_1_gfblup_prediction_all_9001_10000.rds") +T20_1_gfblup_prediction_all_10001_11000=readRDS(file="T20_1_gfblup_prediction_all_10001_11000.rds") +T20_1_gfblup_prediction_all_11001_12419=readRDS(file="T20_1_gfblup_prediction_all_11001_12419.rds") + +T20_1_gfblup_variances_all_1_1000=readRDS(file="T20_1_gfblup_variances_all_1_1000.rds") +T20_1_gfblup_variances_all_1001_2000=readRDS(file="T20_1_gfblup_variances_all_1001_2000.rds") +T20_1_gfblup_variances_all_2001_3000=readRDS(file="T20_1_gfblup_variances_all_2001_3000.rds") +T20_1_gfblup_variances_all_3001_4000=readRDS(file="T20_1_gfblup_variances_all_3001_4000.rds") +T20_1_gfblup_variances_all_4001_5000=readRDS(file="T20_1_gfblup_variances_all_4001_5000.rds") +T20_1_gfblup_variances_all_5001_6000=readRDS(file="T20_1_gfblup_variances_all_5001_6000.rds") +T20_1_gfblup_variances_all_6001_7000=readRDS(file="T20_1_gfblup_variances_all_6001_7000.rds") +T20_1_gfblup_variances_all_7001_8000=readRDS(file="T20_1_gfblup_variances_all_7001_8000.rds") +T20_1_gfblup_variances_all_8001_9000=readRDS(file="T20_1_gfblup_variances_all_8001_9000.rds") +T20_1_gfblup_variances_all_9001_10000=readRDS(file="T20_1_gfblup_variances_all_9001_10000.rds") +T20_1_gfblup_variances_all_10001_11000=readRDS(file="T20_1_gfblup_variances_all_10001_11000.rds") +T20_1_gfblup_variances_all_11001_12419=readRDS(file="T20_1_gfblup_variances_all_11001_12419.rds") + +cycles=length(T20_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T20_1_gfblup_variances_all=rep(list(list()),cycles) +T20_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_1_1000[[r]]) + T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_1001_2000[[r]]) + T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_2001_3000[[r]]) + T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_3001_4000[[r]]) + T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_4001_5000[[r]]) + T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_5001_6000[[r]]) + T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_6001_7000[[r]]) + T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_7001_8000[[r]]) + T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_8001_9000[[r]]) + T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_9001_10000[[r]]) + T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_10001_11000[[r]]) + T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_11001_12419[[r]]) + + T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_1_1000[[r]]) + T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_1001_2000[[r]]) + T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_2001_3000[[r]]) + T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_3001_4000[[r]]) + T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_4001_5000[[r]]) + T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_5001_6000[[r]]) + T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_6001_7000[[r]]) + T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_7001_8000[[r]]) + T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_8001_9000[[r]]) + T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_9001_10000[[r]]) + T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_10001_11000[[r]]) + T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T20_1_gfblup_prediction_all,"T20_1_gfblup_prediction_all.rds") +saveRDS(T20_1_gfblup_variances_all,"T20_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T20_2_gblup_prediction_all_1_1000=readRDS(file="T20_2_gblup_prediction_all_1_1000.rds") +T20_2_gblup_prediction_all_1001_2000=readRDS(file="T20_2_gblup_prediction_all_1001_2000.rds") +T20_2_gblup_prediction_all_2001_3000=readRDS(file="T20_2_gblup_prediction_all_2001_3000.rds") +T20_2_gblup_prediction_all_3001_4000=readRDS(file="T20_2_gblup_prediction_all_3001_4000.rds") +T20_2_gblup_prediction_all_4001_5000=readRDS(file="T20_2_gblup_prediction_all_4001_5000.rds") +T20_2_gblup_prediction_all_5001_6000=readRDS(file="T20_2_gblup_prediction_all_5001_6000.rds") +T20_2_gblup_prediction_all_6001_7000=readRDS(file="T20_2_gblup_prediction_all_6001_7000.rds") +T20_2_gblup_prediction_all_7001_8000=readRDS(file="T20_2_gblup_prediction_all_7001_8000.rds") +T20_2_gblup_prediction_all_8001_9000=readRDS(file="T20_2_gblup_prediction_all_8001_9000.rds") +T20_2_gblup_prediction_all_9001_10000=readRDS(file="T20_2_gblup_prediction_all_9001_10000.rds") +T20_2_gblup_prediction_all_10001_11000=readRDS(file="T20_2_gblup_prediction_all_10001_11000.rds") +T20_2_gblup_prediction_all_11001_12419=readRDS(file="T20_2_gblup_prediction_all_11001_12419.rds") +T20_2_gblup_prediction_all=c(T20_2_gblup_prediction_all_1_1000,T20_2_gblup_prediction_all_1001_2000,T20_2_gblup_prediction_all_2001_3000,T20_2_gblup_prediction_all_3001_4000,T20_2_gblup_prediction_all_4001_5000,T20_2_gblup_prediction_all_5001_6000,T20_2_gblup_prediction_all_6001_7000,T20_2_gblup_prediction_all_7001_8000,T20_2_gblup_prediction_all_8001_9000,T20_2_gblup_prediction_all_9001_10000,T20_2_gblup_prediction_all_10001_11000,T20_2_gblup_prediction_all_11001_12419) + +T20_2_gblup_variances_all_1_1000=readRDS(file="T20_2_gblup_variances_all_1_1000.rds") +T20_2_gblup_variances_all_1001_2000=readRDS(file="T20_2_gblup_variances_all_1001_2000.rds") +T20_2_gblup_variances_all_2001_3000=readRDS(file="T20_2_gblup_variances_all_2001_3000.rds") +T20_2_gblup_variances_all_3001_4000=readRDS(file="T20_2_gblup_variances_all_3001_4000.rds") +T20_2_gblup_variances_all_4001_5000=readRDS(file="T20_2_gblup_variances_all_4001_5000.rds") +T20_2_gblup_variances_all_5001_6000=readRDS(file="T20_2_gblup_variances_all_5001_6000.rds") +T20_2_gblup_variances_all_6001_7000=readRDS(file="T20_2_gblup_variances_all_6001_7000.rds") +T20_2_gblup_variances_all_7001_8000=readRDS(file="T20_2_gblup_variances_all_7001_8000.rds") +T20_2_gblup_variances_all_8001_9000=readRDS(file="T20_2_gblup_variances_all_8001_9000.rds") +T20_2_gblup_variances_all_9001_10000=readRDS(file="T20_2_gblup_variances_all_9001_10000.rds") +T20_2_gblup_variances_all_10001_11000=readRDS(file="T20_2_gblup_variances_all_10001_11000.rds") +T20_2_gblup_variances_all_11001_12419=readRDS(file="T20_2_gblup_variances_all_11001_12419.rds") +T20_2_gblup_variances_all=c(T20_2_gblup_variances_all_1_1000,T20_2_gblup_variances_all_1001_2000,T20_2_gblup_variances_all_2001_3000,T20_2_gblup_variances_all_3001_4000,T20_2_gblup_variances_all_4001_5000,T20_2_gblup_variances_all_5001_6000,T20_2_gblup_variances_all_6001_7000,T20_2_gblup_variances_all_7001_8000,T20_2_gblup_variances_all_8001_9000,T20_2_gblup_variances_all_9001_10000,T20_2_gblup_variances_all_10001_11000,T20_2_gblup_variances_all_11001_12419) + +saveRDS(T20_2_gblup_prediction_all,"T20_2_gblup_prediction_all.rds") +saveRDS(T20_2_gblup_variances_all,"T20_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T20_2_gfblup_prediction_all_1_1000=readRDS(file="T20_2_gfblup_prediction_all_1_1000.rds") +T20_2_gfblup_prediction_all_1001_2000=readRDS(file="T20_2_gfblup_prediction_all_1001_2000.rds") +T20_2_gfblup_prediction_all_2001_3000=readRDS(file="T20_2_gfblup_prediction_all_2001_3000.rds") +T20_2_gfblup_prediction_all_3001_4000=readRDS(file="T20_2_gfblup_prediction_all_3001_4000.rds") +T20_2_gfblup_prediction_all_4001_5000=readRDS(file="T20_2_gfblup_prediction_all_4001_5000.rds") +T20_2_gfblup_prediction_all_5001_6000=readRDS(file="T20_2_gfblup_prediction_all_5001_6000.rds") +T20_2_gfblup_prediction_all_6001_7000=readRDS(file="T20_2_gfblup_prediction_all_6001_7000.rds") +T20_2_gfblup_prediction_all_7001_8000=readRDS(file="T20_2_gfblup_prediction_all_7001_8000.rds") +T20_2_gfblup_prediction_all_8001_9000=readRDS(file="T20_2_gfblup_prediction_all_8001_9000.rds") +T20_2_gfblup_prediction_all_9001_10000=readRDS(file="T20_2_gfblup_prediction_all_9001_10000.rds") +T20_2_gfblup_prediction_all_10001_11000=readRDS(file="T20_2_gfblup_prediction_all_10001_11000.rds") +T20_2_gfblup_prediction_all_11001_12419=readRDS(file="T20_2_gfblup_prediction_all_11001_12419.rds") + +T20_2_gfblup_variances_all_1_1000=readRDS(file="T20_2_gfblup_variances_all_1_1000.rds") +T20_2_gfblup_variances_all_1001_2000=readRDS(file="T20_2_gfblup_variances_all_1001_2000.rds") +T20_2_gfblup_variances_all_2001_3000=readRDS(file="T20_2_gfblup_variances_all_2001_3000.rds") +T20_2_gfblup_variances_all_3001_4000=readRDS(file="T20_2_gfblup_variances_all_3001_4000.rds") +T20_2_gfblup_variances_all_4001_5000=readRDS(file="T20_2_gfblup_variances_all_4001_5000.rds") +T20_2_gfblup_variances_all_5001_6000=readRDS(file="T20_2_gfblup_variances_all_5001_6000.rds") +T20_2_gfblup_variances_all_6001_7000=readRDS(file="T20_2_gfblup_variances_all_6001_7000.rds") +T20_2_gfblup_variances_all_7001_8000=readRDS(file="T20_2_gfblup_variances_all_7001_8000.rds") +T20_2_gfblup_variances_all_8001_9000=readRDS(file="T20_2_gfblup_variances_all_8001_9000.rds") +T20_2_gfblup_variances_all_9001_10000=readRDS(file="T20_2_gfblup_variances_all_9001_10000.rds") +T20_2_gfblup_variances_all_10001_11000=readRDS(file="T20_2_gfblup_variances_all_10001_11000.rds") +T20_2_gfblup_variances_all_11001_12419=readRDS(file="T20_2_gfblup_variances_all_11001_12419.rds") + +cycles=length(T20_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T20_2_gfblup_variances_all=rep(list(list()),cycles) +T20_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_1_1000[[r]]) + T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_1001_2000[[r]]) + T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_2001_3000[[r]]) + T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_3001_4000[[r]]) + T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_4001_5000[[r]]) + T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_5001_6000[[r]]) + T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_6001_7000[[r]]) + T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_7001_8000[[r]]) + T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_8001_9000[[r]]) + T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_9001_10000[[r]]) + T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_10001_11000[[r]]) + T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_11001_12419[[r]]) + + T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_1_1000[[r]]) + T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_1001_2000[[r]]) + T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_2001_3000[[r]]) + T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_3001_4000[[r]]) + T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_4001_5000[[r]]) + T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_5001_6000[[r]]) + T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_6001_7000[[r]]) + T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_7001_8000[[r]]) + T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_8001_9000[[r]]) + T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_9001_10000[[r]]) + T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_10001_11000[[r]]) + T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(T20_2_gfblup_prediction_all,"T20_2_gfblup_prediction_all.rds") +saveRDS(T20_2_gfblup_variances_all,"T20_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + diff --git a/code/using_COEX/pla/gblup_vs_gfblup_using_coexpression_analysis1.R b/code/using_COEX/pla/gblup_vs_gfblup_using_coexpression_analysis1.R index 2e82e61ed45871e35b174e76b39add5207afcbfc..816f0dc1d50d3548e886424f019176b11daf1cd3 100644 --- a/code/using_COEX/pla/gblup_vs_gfblup_using_coexpression_analysis1.R +++ b/code/using_COEX/pla/gblup_vs_gfblup_using_coexpression_analysis1.R @@ -2,11 +2,27 @@ ################################################################################################################################## # A N A L Y S I S ################################################################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_COEX/pla/8fold/") - -all_coexpression_clusters <-as.data.frame(read.table(file ="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/ath_gene_clusters.txt", header=TRUE, sep="",strip.white=TRUE)) -coex_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/coex_markers_number.rds") -coex_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/coex_markers.rds") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} +setwd(paste0(wdir,"/",wd,"/8fold/")); +################################################################################################################################## +all_coexpression_clusters <-as.data.frame(read.table(file ="../data/priors/coexpression/ath_gene_clusters.txt", header=TRUE, sep="",strip.white=TRUE)) +coex_markers_number=readRDS(file="../data/priors/coexpression/coex_markers_number.rds") +coex_markers=readRDS(file="../data/priors/coexpression/coex_markers.rds") ################################################################################################################################### T20_2_gblup_variances_all=readRDS(file="./T20_2_gblup_variances_all.rds") T20_2_gblup_prediction_all=readRDS(file="./T20_2_gblup_prediction_all.rds") diff --git a/code/using_COEX/psii/8fold/combine.R b/code/using_COEX/psii/8fold/combine.R new file mode 100644 index 0000000000000000000000000000000000000000..cbc91f9b19dfd7cf79181a6dd069a26c8142966b --- /dev/null +++ b/code/using_COEX/psii/8fold/combine.R @@ -0,0 +1,1766 @@ +################################################################################################################################## +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} +setwd(paste0(wdir,"/",wd)); +################################################################################################################################## + +L1_1_gblup_prediction_all_1_1000=readRDS(file="L1_1_gblup_prediction_all_1_1000.rds") +L1_1_gblup_prediction_all_1001_2000=readRDS(file="L1_1_gblup_prediction_all_1001_2000.rds") +L1_1_gblup_prediction_all_2001_3000=readRDS(file="L1_1_gblup_prediction_all_2001_3000.rds") +L1_1_gblup_prediction_all_3001_4000=readRDS(file="L1_1_gblup_prediction_all_3001_4000.rds") +L1_1_gblup_prediction_all_4001_5000=readRDS(file="L1_1_gblup_prediction_all_4001_5000.rds") +L1_1_gblup_prediction_all_5001_6000=readRDS(file="L1_1_gblup_prediction_all_5001_6000.rds") +L1_1_gblup_prediction_all_6001_7000=readRDS(file="L1_1_gblup_prediction_all_6001_7000.rds") +L1_1_gblup_prediction_all_7001_8000=readRDS(file="L1_1_gblup_prediction_all_7001_8000.rds") +L1_1_gblup_prediction_all_8001_9000=readRDS(file="L1_1_gblup_prediction_all_8001_9000.rds") +L1_1_gblup_prediction_all_9001_10000=readRDS(file="L1_1_gblup_prediction_all_9001_10000.rds") +L1_1_gblup_prediction_all_10001_11000=readRDS(file="L1_1_gblup_prediction_all_10001_11000.rds") +L1_1_gblup_prediction_all_11001_12419=readRDS(file="L1_1_gblup_prediction_all_11001_12419.rds") +L1_1_gblup_prediction_all=c(L1_1_gblup_prediction_all_1_1000,L1_1_gblup_prediction_all_1001_2000,L1_1_gblup_prediction_all_2001_3000,L1_1_gblup_prediction_all_3001_4000,L1_1_gblup_prediction_all_4001_5000,L1_1_gblup_prediction_all_5001_6000,L1_1_gblup_prediction_all_6001_7000,L1_1_gblup_prediction_all_7001_8000,L1_1_gblup_prediction_all_8001_9000,L1_1_gblup_prediction_all_9001_10000,L1_1_gblup_prediction_all_10001_11000,L1_1_gblup_prediction_all_11001_12419) + +L1_1_gblup_variances_all_1_1000=readRDS(file="L1_1_gblup_variances_all_1_1000.rds") +L1_1_gblup_variances_all_1001_2000=readRDS(file="L1_1_gblup_variances_all_1001_2000.rds") +L1_1_gblup_variances_all_2001_3000=readRDS(file="L1_1_gblup_variances_all_2001_3000.rds") +L1_1_gblup_variances_all_3001_4000=readRDS(file="L1_1_gblup_variances_all_3001_4000.rds") +L1_1_gblup_variances_all_4001_5000=readRDS(file="L1_1_gblup_variances_all_4001_5000.rds") +L1_1_gblup_variances_all_5001_6000=readRDS(file="L1_1_gblup_variances_all_5001_6000.rds") +L1_1_gblup_variances_all_6001_7000=readRDS(file="L1_1_gblup_variances_all_6001_7000.rds") +L1_1_gblup_variances_all_7001_8000=readRDS(file="L1_1_gblup_variances_all_7001_8000.rds") +L1_1_gblup_variances_all_8001_9000=readRDS(file="L1_1_gblup_variances_all_8001_9000.rds") +L1_1_gblup_variances_all_9001_10000=readRDS(file="L1_1_gblup_variances_all_9001_10000.rds") +L1_1_gblup_variances_all_10001_11000=readRDS(file="L1_1_gblup_variances_all_10001_11000.rds") +L1_1_gblup_variances_all_11001_12419=readRDS(file="L1_1_gblup_variances_all_11001_12419.rds") +L1_1_gblup_variances_all=c(L1_1_gblup_variances_all_1_1000,L1_1_gblup_variances_all_1001_2000,L1_1_gblup_variances_all_2001_3000,L1_1_gblup_variances_all_3001_4000,L1_1_gblup_variances_all_4001_5000,L1_1_gblup_variances_all_5001_6000,L1_1_gblup_variances_all_6001_7000,L1_1_gblup_variances_all_7001_8000,L1_1_gblup_variances_all_8001_9000,L1_1_gblup_variances_all_9001_10000,L1_1_gblup_variances_all_10001_11000,L1_1_gblup_variances_all_11001_12419) + +saveRDS(L1_1_gblup_prediction_all,"L1_1_gblup_prediction_all.rds") +saveRDS(L1_1_gblup_variances_all,"L1_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +L1_1_gfblup_prediction_all_1_1000=readRDS(file="L1_1_gfblup_prediction_all_1_1000.rds") +L1_1_gfblup_prediction_all_1001_2000=readRDS(file="L1_1_gfblup_prediction_all_1001_2000.rds") +L1_1_gfblup_prediction_all_2001_3000=readRDS(file="L1_1_gfblup_prediction_all_2001_3000.rds") +L1_1_gfblup_prediction_all_3001_4000=readRDS(file="L1_1_gfblup_prediction_all_3001_4000.rds") +L1_1_gfblup_prediction_all_4001_5000=readRDS(file="L1_1_gfblup_prediction_all_4001_5000.rds") +L1_1_gfblup_prediction_all_5001_6000=readRDS(file="L1_1_gfblup_prediction_all_5001_6000.rds") +L1_1_gfblup_prediction_all_6001_7000=readRDS(file="L1_1_gfblup_prediction_all_6001_7000.rds") +L1_1_gfblup_prediction_all_7001_8000=readRDS(file="L1_1_gfblup_prediction_all_7001_8000.rds") +L1_1_gfblup_prediction_all_8001_9000=readRDS(file="L1_1_gfblup_prediction_all_8001_9000.rds") +L1_1_gfblup_prediction_all_9001_10000=readRDS(file="L1_1_gfblup_prediction_all_9001_10000.rds") +L1_1_gfblup_prediction_all_10001_11000=readRDS(file="L1_1_gfblup_prediction_all_10001_11000.rds") +L1_1_gfblup_prediction_all_11001_12419=readRDS(file="L1_1_gfblup_prediction_all_11001_12419.rds") + +L1_1_gfblup_variances_all_1_1000=readRDS(file="L1_1_gfblup_variances_all_1_1000.rds") +L1_1_gfblup_variances_all_1001_2000=readRDS(file="L1_1_gfblup_variances_all_1001_2000.rds") +L1_1_gfblup_variances_all_2001_3000=readRDS(file="L1_1_gfblup_variances_all_2001_3000.rds") +L1_1_gfblup_variances_all_3001_4000=readRDS(file="L1_1_gfblup_variances_all_3001_4000.rds") +L1_1_gfblup_variances_all_4001_5000=readRDS(file="L1_1_gfblup_variances_all_4001_5000.rds") +L1_1_gfblup_variances_all_5001_6000=readRDS(file="L1_1_gfblup_variances_all_5001_6000.rds") +L1_1_gfblup_variances_all_6001_7000=readRDS(file="L1_1_gfblup_variances_all_6001_7000.rds") +L1_1_gfblup_variances_all_7001_8000=readRDS(file="L1_1_gfblup_variances_all_7001_8000.rds") +L1_1_gfblup_variances_all_8001_9000=readRDS(file="L1_1_gfblup_variances_all_8001_9000.rds") +L1_1_gfblup_variances_all_9001_10000=readRDS(file="L1_1_gfblup_variances_all_9001_10000.rds") +L1_1_gfblup_variances_all_10001_11000=readRDS(file="L1_1_gfblup_variances_all_10001_11000.rds") +L1_1_gfblup_variances_all_11001_12419=readRDS(file="L1_1_gfblup_variances_all_11001_12419.rds") + +cycles=length(L1_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +L1_1_gfblup_variances_all=rep(list(list()),cycles) +L1_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_1_1000[[r]]) + L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_1001_2000[[r]]) + L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_2001_3000[[r]]) + L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_3001_4000[[r]]) + L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_4001_5000[[r]]) + L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_5001_6000[[r]]) + L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_6001_7000[[r]]) + L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_7001_8000[[r]]) + L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_8001_9000[[r]]) + L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_9001_10000[[r]]) + L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_10001_11000[[r]]) + L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_11001_12419[[r]]) + + L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_1_1000[[r]]) + L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_1001_2000[[r]]) + L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_2001_3000[[r]]) + L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_3001_4000[[r]]) + L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_4001_5000[[r]]) + L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_5001_6000[[r]]) + L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_6001_7000[[r]]) + L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_7001_8000[[r]]) + L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_8001_9000[[r]]) + L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_9001_10000[[r]]) + L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_10001_11000[[r]]) + L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(L1_1_gfblup_prediction_all,"L1_1_gfblup_prediction_all.rds") +saveRDS(L1_1_gfblup_variances_all,"L1_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +L1_2_gblup_prediction_all_1_1000=readRDS(file="L1_2_gblup_prediction_all_1_1000.rds") +L1_2_gblup_prediction_all_1001_2000=readRDS(file="L1_2_gblup_prediction_all_1001_2000.rds") +L1_2_gblup_prediction_all_2001_3000=readRDS(file="L1_2_gblup_prediction_all_2001_3000.rds") +L1_2_gblup_prediction_all_3001_4000=readRDS(file="L1_2_gblup_prediction_all_3001_4000.rds") +L1_2_gblup_prediction_all_4001_5000=readRDS(file="L1_2_gblup_prediction_all_4001_5000.rds") +L1_2_gblup_prediction_all_5001_6000=readRDS(file="L1_2_gblup_prediction_all_5001_6000.rds") +L1_2_gblup_prediction_all_6001_7000=readRDS(file="L1_2_gblup_prediction_all_6001_7000.rds") +L1_2_gblup_prediction_all_7001_8000=readRDS(file="L1_2_gblup_prediction_all_7001_8000.rds") +L1_2_gblup_prediction_all_8001_9000=readRDS(file="L1_2_gblup_prediction_all_8001_9000.rds") +L1_2_gblup_prediction_all_9001_10000=readRDS(file="L1_2_gblup_prediction_all_9001_10000.rds") +L1_2_gblup_prediction_all_10001_11000=readRDS(file="L1_2_gblup_prediction_all_10001_11000.rds") +L1_2_gblup_prediction_all_11001_12419=readRDS(file="L1_2_gblup_prediction_all_11001_12419.rds") +L1_2_gblup_prediction_all=c(L1_2_gblup_prediction_all_1_1000,L1_2_gblup_prediction_all_1001_2000,L1_2_gblup_prediction_all_2001_3000,L1_2_gblup_prediction_all_3001_4000,L1_2_gblup_prediction_all_4001_5000,L1_2_gblup_prediction_all_5001_6000,L1_2_gblup_prediction_all_6001_7000,L1_2_gblup_prediction_all_7001_8000,L1_2_gblup_prediction_all_8001_9000,L1_2_gblup_prediction_all_9001_10000,L1_2_gblup_prediction_all_10001_11000,L1_2_gblup_prediction_all_11001_12419) + +L1_2_gblup_variances_all_1_1000=readRDS(file="L1_2_gblup_variances_all_1_1000.rds") +L1_2_gblup_variances_all_1001_2000=readRDS(file="L1_2_gblup_variances_all_1001_2000.rds") +L1_2_gblup_variances_all_2001_3000=readRDS(file="L1_2_gblup_variances_all_2001_3000.rds") +L1_2_gblup_variances_all_3001_4000=readRDS(file="L1_2_gblup_variances_all_3001_4000.rds") +L1_2_gblup_variances_all_4001_5000=readRDS(file="L1_2_gblup_variances_all_4001_5000.rds") +L1_2_gblup_variances_all_5001_6000=readRDS(file="L1_2_gblup_variances_all_5001_6000.rds") +L1_2_gblup_variances_all_6001_7000=readRDS(file="L1_2_gblup_variances_all_6001_7000.rds") +L1_2_gblup_variances_all_7001_8000=readRDS(file="L1_2_gblup_variances_all_7001_8000.rds") +L1_2_gblup_variances_all_8001_9000=readRDS(file="L1_2_gblup_variances_all_8001_9000.rds") +L1_2_gblup_variances_all_9001_10000=readRDS(file="L1_2_gblup_variances_all_9001_10000.rds") +L1_2_gblup_variances_all_10001_11000=readRDS(file="L1_2_gblup_variances_all_10001_11000.rds") +L1_2_gblup_variances_all_11001_12419=readRDS(file="L1_2_gblup_variances_all_11001_12419.rds") +L1_2_gblup_variances_all=c(L1_2_gblup_variances_all_1_1000,L1_2_gblup_variances_all_1001_2000,L1_2_gblup_variances_all_2001_3000,L1_2_gblup_variances_all_3001_4000,L1_2_gblup_variances_all_4001_5000,L1_2_gblup_variances_all_5001_6000,L1_2_gblup_variances_all_6001_7000,L1_2_gblup_variances_all_7001_8000,L1_2_gblup_variances_all_8001_9000,L1_2_gblup_variances_all_9001_10000,L1_2_gblup_variances_all_10001_11000,L1_2_gblup_variances_all_11001_12419) + +saveRDS(L1_2_gblup_prediction_all,"L1_2_gblup_prediction_all.rds") +saveRDS(L1_2_gblup_variances_all,"L1_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +L1_2_gfblup_prediction_all_1_1000=readRDS(file="L1_2_gfblup_prediction_all_1_1000.rds") +L1_2_gfblup_prediction_all_1001_2000=readRDS(file="L1_2_gfblup_prediction_all_1001_2000.rds") +L1_2_gfblup_prediction_all_2001_3000=readRDS(file="L1_2_gfblup_prediction_all_2001_3000.rds") +L1_2_gfblup_prediction_all_3001_4000=readRDS(file="L1_2_gfblup_prediction_all_3001_4000.rds") +L1_2_gfblup_prediction_all_4001_5000=readRDS(file="L1_2_gfblup_prediction_all_4001_5000.rds") +L1_2_gfblup_prediction_all_5001_6000=readRDS(file="L1_2_gfblup_prediction_all_5001_6000.rds") +L1_2_gfblup_prediction_all_6001_7000=readRDS(file="L1_2_gfblup_prediction_all_6001_7000.rds") +L1_2_gfblup_prediction_all_7001_8000=readRDS(file="L1_2_gfblup_prediction_all_7001_8000.rds") +L1_2_gfblup_prediction_all_8001_9000=readRDS(file="L1_2_gfblup_prediction_all_8001_9000.rds") +L1_2_gfblup_prediction_all_9001_10000=readRDS(file="L1_2_gfblup_prediction_all_9001_10000.rds") +L1_2_gfblup_prediction_all_10001_11000=readRDS(file="L1_2_gfblup_prediction_all_10001_11000.rds") +L1_2_gfblup_prediction_all_11001_12419=readRDS(file="L1_2_gfblup_prediction_all_11001_12419.rds") + +L1_2_gfblup_variances_all_1_1000=readRDS(file="L1_2_gfblup_variances_all_1_1000.rds") +L1_2_gfblup_variances_all_1001_2000=readRDS(file="L1_2_gfblup_variances_all_1001_2000.rds") +L1_2_gfblup_variances_all_2001_3000=readRDS(file="L1_2_gfblup_variances_all_2001_3000.rds") +L1_2_gfblup_variances_all_3001_4000=readRDS(file="L1_2_gfblup_variances_all_3001_4000.rds") +L1_2_gfblup_variances_all_4001_5000=readRDS(file="L1_2_gfblup_variances_all_4001_5000.rds") +L1_2_gfblup_variances_all_5001_6000=readRDS(file="L1_2_gfblup_variances_all_5001_6000.rds") +L1_2_gfblup_variances_all_6001_7000=readRDS(file="L1_2_gfblup_variances_all_6001_7000.rds") +L1_2_gfblup_variances_all_7001_8000=readRDS(file="L1_2_gfblup_variances_all_7001_8000.rds") +L1_2_gfblup_variances_all_8001_9000=readRDS(file="L1_2_gfblup_variances_all_8001_9000.rds") +L1_2_gfblup_variances_all_9001_10000=readRDS(file="L1_2_gfblup_variances_all_9001_10000.rds") +L1_2_gfblup_variances_all_10001_11000=readRDS(file="L1_2_gfblup_variances_all_10001_11000.rds") +L1_2_gfblup_variances_all_11001_12419=readRDS(file="L1_2_gfblup_variances_all_11001_12419.rds") + +cycles=length(L1_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +L1_2_gfblup_variances_all=rep(list(list()),cycles) +L1_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_1_1000[[r]]) + L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_1001_2000[[r]]) + L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_2001_3000[[r]]) + L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_3001_4000[[r]]) + L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_4001_5000[[r]]) + L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_5001_6000[[r]]) + L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_6001_7000[[r]]) + L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_7001_8000[[r]]) + L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_8001_9000[[r]]) + L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_9001_10000[[r]]) + L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_10001_11000[[r]]) + L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_11001_12419[[r]]) + + L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_1_1000[[r]]) + L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_1001_2000[[r]]) + L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_2001_3000[[r]]) + L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_3001_4000[[r]]) + L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_4001_5000[[r]]) + L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_5001_6000[[r]]) + L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_6001_7000[[r]]) + L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_7001_8000[[r]]) + L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_8001_9000[[r]]) + L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_9001_10000[[r]]) + L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_10001_11000[[r]]) + L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(L1_2_gfblup_prediction_all,"L1_2_gfblup_prediction_all.rds") +saveRDS(L1_2_gfblup_variances_all,"L1_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +L1_3_gblup_prediction_all_1_1000=readRDS(file="L1_3_gblup_prediction_all_1_1000.rds") +L1_3_gblup_prediction_all_1001_2000=readRDS(file="L1_3_gblup_prediction_all_1001_2000.rds") +L1_3_gblup_prediction_all_2001_3000=readRDS(file="L1_3_gblup_prediction_all_2001_3000.rds") +L1_3_gblup_prediction_all_3001_4000=readRDS(file="L1_3_gblup_prediction_all_3001_4000.rds") +L1_3_gblup_prediction_all_4001_5000=readRDS(file="L1_3_gblup_prediction_all_4001_5000.rds") +L1_3_gblup_prediction_all_5001_6000=readRDS(file="L1_3_gblup_prediction_all_5001_6000.rds") +L1_3_gblup_prediction_all_6001_7000=readRDS(file="L1_3_gblup_prediction_all_6001_7000.rds") +L1_3_gblup_prediction_all_7001_8000=readRDS(file="L1_3_gblup_prediction_all_7001_8000.rds") +L1_3_gblup_prediction_all_8001_9000=readRDS(file="L1_3_gblup_prediction_all_8001_9000.rds") +L1_3_gblup_prediction_all_9001_10000=readRDS(file="L1_3_gblup_prediction_all_9001_10000.rds") +L1_3_gblup_prediction_all_10001_11000=readRDS(file="L1_3_gblup_prediction_all_10001_11000.rds") +L1_3_gblup_prediction_all_11001_12419=readRDS(file="L1_3_gblup_prediction_all_11001_12419.rds") +L1_3_gblup_prediction_all=c(L1_3_gblup_prediction_all_1_1000,L1_3_gblup_prediction_all_1001_2000,L1_3_gblup_prediction_all_2001_3000,L1_3_gblup_prediction_all_3001_4000,L1_3_gblup_prediction_all_4001_5000,L1_3_gblup_prediction_all_5001_6000,L1_3_gblup_prediction_all_6001_7000,L1_3_gblup_prediction_all_7001_8000,L1_3_gblup_prediction_all_8001_9000,L1_3_gblup_prediction_all_9001_10000,L1_3_gblup_prediction_all_10001_11000,L1_3_gblup_prediction_all_11001_12419) + +L1_3_gblup_variances_all_1_1000=readRDS(file="L1_3_gblup_variances_all_1_1000.rds") +L1_3_gblup_variances_all_1001_2000=readRDS(file="L1_3_gblup_variances_all_1001_2000.rds") +L1_3_gblup_variances_all_2001_3000=readRDS(file="L1_3_gblup_variances_all_2001_3000.rds") +L1_3_gblup_variances_all_3001_4000=readRDS(file="L1_3_gblup_variances_all_3001_4000.rds") +L1_3_gblup_variances_all_4001_5000=readRDS(file="L1_3_gblup_variances_all_4001_5000.rds") +L1_3_gblup_variances_all_5001_6000=readRDS(file="L1_3_gblup_variances_all_5001_6000.rds") +L1_3_gblup_variances_all_6001_7000=readRDS(file="L1_3_gblup_variances_all_6001_7000.rds") +L1_3_gblup_variances_all_7001_8000=readRDS(file="L1_3_gblup_variances_all_7001_8000.rds") +L1_3_gblup_variances_all_8001_9000=readRDS(file="L1_3_gblup_variances_all_8001_9000.rds") +L1_3_gblup_variances_all_9001_10000=readRDS(file="L1_3_gblup_variances_all_9001_10000.rds") +L1_3_gblup_variances_all_10001_11000=readRDS(file="L1_3_gblup_variances_all_10001_11000.rds") +L1_3_gblup_variances_all_11001_12419=readRDS(file="L1_3_gblup_variances_all_11001_12419.rds") +L1_3_gblup_variances_all=c(L1_3_gblup_variances_all_1_1000,L1_3_gblup_variances_all_1001_2000,L1_3_gblup_variances_all_2001_3000,L1_3_gblup_variances_all_3001_4000,L1_3_gblup_variances_all_4001_5000,L1_3_gblup_variances_all_5001_6000,L1_3_gblup_variances_all_6001_7000,L1_3_gblup_variances_all_7001_8000,L1_3_gblup_variances_all_8001_9000,L1_3_gblup_variances_all_9001_10000,L1_3_gblup_variances_all_10001_11000,L1_3_gblup_variances_all_11001_12419) + +saveRDS(L1_3_gblup_prediction_all,"L1_3_gblup_prediction_all.rds") +saveRDS(L1_3_gblup_variances_all,"L1_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +L1_3_gfblup_prediction_all_1_1000=readRDS(file="L1_3_gfblup_prediction_all_1_1000.rds") +L1_3_gfblup_prediction_all_1001_2000=readRDS(file="L1_3_gfblup_prediction_all_1001_2000.rds") +L1_3_gfblup_prediction_all_2001_3000=readRDS(file="L1_3_gfblup_prediction_all_2001_3000.rds") +L1_3_gfblup_prediction_all_3001_4000=readRDS(file="L1_3_gfblup_prediction_all_3001_4000.rds") +L1_3_gfblup_prediction_all_4001_5000=readRDS(file="L1_3_gfblup_prediction_all_4001_5000.rds") +L1_3_gfblup_prediction_all_5001_6000=readRDS(file="L1_3_gfblup_prediction_all_5001_6000.rds") +L1_3_gfblup_prediction_all_6001_7000=readRDS(file="L1_3_gfblup_prediction_all_6001_7000.rds") +L1_3_gfblup_prediction_all_7001_8000=readRDS(file="L1_3_gfblup_prediction_all_7001_8000.rds") +L1_3_gfblup_prediction_all_8001_9000=readRDS(file="L1_3_gfblup_prediction_all_8001_9000.rds") +L1_3_gfblup_prediction_all_9001_10000=readRDS(file="L1_3_gfblup_prediction_all_9001_10000.rds") +L1_3_gfblup_prediction_all_10001_11000=readRDS(file="L1_3_gfblup_prediction_all_10001_11000.rds") +L1_3_gfblup_prediction_all_11001_12419=readRDS(file="L1_3_gfblup_prediction_all_11001_12419.rds") + +L1_3_gfblup_variances_all_1_1000=readRDS(file="L1_3_gfblup_variances_all_1_1000.rds") +L1_3_gfblup_variances_all_1001_2000=readRDS(file="L1_3_gfblup_variances_all_1001_2000.rds") +L1_3_gfblup_variances_all_2001_3000=readRDS(file="L1_3_gfblup_variances_all_2001_3000.rds") +L1_3_gfblup_variances_all_3001_4000=readRDS(file="L1_3_gfblup_variances_all_3001_4000.rds") +L1_3_gfblup_variances_all_4001_5000=readRDS(file="L1_3_gfblup_variances_all_4001_5000.rds") +L1_3_gfblup_variances_all_5001_6000=readRDS(file="L1_3_gfblup_variances_all_5001_6000.rds") +L1_3_gfblup_variances_all_6001_7000=readRDS(file="L1_3_gfblup_variances_all_6001_7000.rds") +L1_3_gfblup_variances_all_7001_8000=readRDS(file="L1_3_gfblup_variances_all_7001_8000.rds") +L1_3_gfblup_variances_all_8001_9000=readRDS(file="L1_3_gfblup_variances_all_8001_9000.rds") +L1_3_gfblup_variances_all_9001_10000=readRDS(file="L1_3_gfblup_variances_all_9001_10000.rds") +L1_3_gfblup_variances_all_10001_11000=readRDS(file="L1_3_gfblup_variances_all_10001_11000.rds") +L1_3_gfblup_variances_all_11001_12419=readRDS(file="L1_3_gfblup_variances_all_11001_12419.rds") + +cycles=length(L1_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +L1_3_gfblup_variances_all=rep(list(list()),cycles) +L1_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_1_1000[[r]]) + L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_1001_2000[[r]]) + L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_2001_3000[[r]]) + L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_3001_4000[[r]]) + L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_4001_5000[[r]]) + L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_5001_6000[[r]]) + L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_6001_7000[[r]]) + L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_7001_8000[[r]]) + L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_8001_9000[[r]]) + L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_9001_10000[[r]]) + L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_10001_11000[[r]]) + L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_11001_12419[[r]]) + + L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_1_1000[[r]]) + L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_1001_2000[[r]]) + L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_2001_3000[[r]]) + L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_3001_4000[[r]]) + L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_4001_5000[[r]]) + L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_5001_6000[[r]]) + L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_6001_7000[[r]]) + L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_7001_8000[[r]]) + L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_8001_9000[[r]]) + L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_9001_10000[[r]]) + L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_10001_11000[[r]]) + L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(L1_3_gfblup_prediction_all,"L1_3_gfblup_prediction_all.rds") +saveRDS(L1_3_gfblup_variances_all,"L1_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +L2_1_gblup_prediction_all_1_1000=readRDS(file="L2_1_gblup_prediction_all_1_1000.rds") +L2_1_gblup_prediction_all_1001_2000=readRDS(file="L2_1_gblup_prediction_all_1001_2000.rds") +L2_1_gblup_prediction_all_2001_3000=readRDS(file="L2_1_gblup_prediction_all_2001_3000.rds") +L2_1_gblup_prediction_all_3001_4000=readRDS(file="L2_1_gblup_prediction_all_3001_4000.rds") +L2_1_gblup_prediction_all_4001_5000=readRDS(file="L2_1_gblup_prediction_all_4001_5000.rds") +L2_1_gblup_prediction_all_5001_6000=readRDS(file="L2_1_gblup_prediction_all_5001_6000.rds") +L2_1_gblup_prediction_all_6001_7000=readRDS(file="L2_1_gblup_prediction_all_6001_7000.rds") +L2_1_gblup_prediction_all_7001_8000=readRDS(file="L2_1_gblup_prediction_all_7001_8000.rds") +L2_1_gblup_prediction_all_8001_9000=readRDS(file="L2_1_gblup_prediction_all_8001_9000.rds") +L2_1_gblup_prediction_all_9001_10000=readRDS(file="L2_1_gblup_prediction_all_9001_10000.rds") +L2_1_gblup_prediction_all_10001_11000=readRDS(file="L2_1_gblup_prediction_all_10001_11000.rds") +L2_1_gblup_prediction_all_11001_12419=readRDS(file="L2_1_gblup_prediction_all_11001_12419.rds") +L2_1_gblup_prediction_all=c(L2_1_gblup_prediction_all_1_1000,L2_1_gblup_prediction_all_1001_2000,L2_1_gblup_prediction_all_2001_3000,L2_1_gblup_prediction_all_3001_4000,L2_1_gblup_prediction_all_4001_5000,L2_1_gblup_prediction_all_5001_6000,L2_1_gblup_prediction_all_6001_7000,L2_1_gblup_prediction_all_7001_8000,L2_1_gblup_prediction_all_8001_9000,L2_1_gblup_prediction_all_9001_10000,L2_1_gblup_prediction_all_10001_11000,L2_1_gblup_prediction_all_11001_12419) + +L2_1_gblup_variances_all_1_1000=readRDS(file="L2_1_gblup_variances_all_1_1000.rds") +L2_1_gblup_variances_all_1001_2000=readRDS(file="L2_1_gblup_variances_all_1001_2000.rds") +L2_1_gblup_variances_all_2001_3000=readRDS(file="L2_1_gblup_variances_all_2001_3000.rds") +L2_1_gblup_variances_all_3001_4000=readRDS(file="L2_1_gblup_variances_all_3001_4000.rds") +L2_1_gblup_variances_all_4001_5000=readRDS(file="L2_1_gblup_variances_all_4001_5000.rds") +L2_1_gblup_variances_all_5001_6000=readRDS(file="L2_1_gblup_variances_all_5001_6000.rds") +L2_1_gblup_variances_all_6001_7000=readRDS(file="L2_1_gblup_variances_all_6001_7000.rds") +L2_1_gblup_variances_all_7001_8000=readRDS(file="L2_1_gblup_variances_all_7001_8000.rds") +L2_1_gblup_variances_all_8001_9000=readRDS(file="L2_1_gblup_variances_all_8001_9000.rds") +L2_1_gblup_variances_all_9001_10000=readRDS(file="L2_1_gblup_variances_all_9001_10000.rds") +L2_1_gblup_variances_all_10001_11000=readRDS(file="L2_1_gblup_variances_all_10001_11000.rds") +L2_1_gblup_variances_all_11001_12419=readRDS(file="L2_1_gblup_variances_all_11001_12419.rds") +L2_1_gblup_variances_all=c(L2_1_gblup_variances_all_1_1000,L2_1_gblup_variances_all_1001_2000,L2_1_gblup_variances_all_2001_3000,L2_1_gblup_variances_all_3001_4000,L2_1_gblup_variances_all_4001_5000,L2_1_gblup_variances_all_5001_6000,L2_1_gblup_variances_all_6001_7000,L2_1_gblup_variances_all_7001_8000,L2_1_gblup_variances_all_8001_9000,L2_1_gblup_variances_all_9001_10000,L2_1_gblup_variances_all_10001_11000,L2_1_gblup_variances_all_11001_12419) + +saveRDS(L2_1_gblup_prediction_all,"L2_1_gblup_prediction_all.rds") +saveRDS(L2_1_gblup_variances_all,"L2_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +L2_1_gfblup_prediction_all_1_1000=readRDS(file="L2_1_gfblup_prediction_all_1_1000.rds") +L2_1_gfblup_prediction_all_1001_2000=readRDS(file="L2_1_gfblup_prediction_all_1001_2000.rds") +L2_1_gfblup_prediction_all_2001_3000=readRDS(file="L2_1_gfblup_prediction_all_2001_3000.rds") +L2_1_gfblup_prediction_all_3001_4000=readRDS(file="L2_1_gfblup_prediction_all_3001_4000.rds") +L2_1_gfblup_prediction_all_4001_5000=readRDS(file="L2_1_gfblup_prediction_all_4001_5000.rds") +L2_1_gfblup_prediction_all_5001_6000=readRDS(file="L2_1_gfblup_prediction_all_5001_6000.rds") +L2_1_gfblup_prediction_all_6001_7000=readRDS(file="L2_1_gfblup_prediction_all_6001_7000.rds") +L2_1_gfblup_prediction_all_7001_8000=readRDS(file="L2_1_gfblup_prediction_all_7001_8000.rds") +L2_1_gfblup_prediction_all_8001_9000=readRDS(file="L2_1_gfblup_prediction_all_8001_9000.rds") +L2_1_gfblup_prediction_all_9001_10000=readRDS(file="L2_1_gfblup_prediction_all_9001_10000.rds") +L2_1_gfblup_prediction_all_10001_11000=readRDS(file="L2_1_gfblup_prediction_all_10001_11000.rds") +L2_1_gfblup_prediction_all_11001_12419=readRDS(file="L2_1_gfblup_prediction_all_11001_12419.rds") + +L2_1_gfblup_variances_all_1_1000=readRDS(file="L2_1_gfblup_variances_all_1_1000.rds") +L2_1_gfblup_variances_all_1001_2000=readRDS(file="L2_1_gfblup_variances_all_1001_2000.rds") +L2_1_gfblup_variances_all_2001_3000=readRDS(file="L2_1_gfblup_variances_all_2001_3000.rds") +L2_1_gfblup_variances_all_3001_4000=readRDS(file="L2_1_gfblup_variances_all_3001_4000.rds") +L2_1_gfblup_variances_all_4001_5000=readRDS(file="L2_1_gfblup_variances_all_4001_5000.rds") +L2_1_gfblup_variances_all_5001_6000=readRDS(file="L2_1_gfblup_variances_all_5001_6000.rds") +L2_1_gfblup_variances_all_6001_7000=readRDS(file="L2_1_gfblup_variances_all_6001_7000.rds") +L2_1_gfblup_variances_all_7001_8000=readRDS(file="L2_1_gfblup_variances_all_7001_8000.rds") +L2_1_gfblup_variances_all_8001_9000=readRDS(file="L2_1_gfblup_variances_all_8001_9000.rds") +L2_1_gfblup_variances_all_9001_10000=readRDS(file="L2_1_gfblup_variances_all_9001_10000.rds") +L2_1_gfblup_variances_all_10001_11000=readRDS(file="L2_1_gfblup_variances_all_10001_11000.rds") +L2_1_gfblup_variances_all_11001_12419=readRDS(file="L2_1_gfblup_variances_all_11001_12419.rds") + +cycles=length(L2_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +L2_1_gfblup_variances_all=rep(list(list()),cycles) +L2_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_1_1000[[r]]) + L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_1001_2000[[r]]) + L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_2001_3000[[r]]) + L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_3001_4000[[r]]) + L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_4001_5000[[r]]) + L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_5001_6000[[r]]) + L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_6001_7000[[r]]) + L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_7001_8000[[r]]) + L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_8001_9000[[r]]) + L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_9001_10000[[r]]) + L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_10001_11000[[r]]) + L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_11001_12419[[r]]) + + L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_1_1000[[r]]) + L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_1001_2000[[r]]) + L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_2001_3000[[r]]) + L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_3001_4000[[r]]) + L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_4001_5000[[r]]) + L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_5001_6000[[r]]) + L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_6001_7000[[r]]) + L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_7001_8000[[r]]) + L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_8001_9000[[r]]) + L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_9001_10000[[r]]) + L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_10001_11000[[r]]) + L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(L2_1_gfblup_prediction_all,"L2_1_gfblup_prediction_all.rds") +saveRDS(L2_1_gfblup_variances_all,"L2_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +L2_2_gblup_prediction_all_1_1000=readRDS(file="L2_2_gblup_prediction_all_1_1000.rds") +L2_2_gblup_prediction_all_1001_2000=readRDS(file="L2_2_gblup_prediction_all_1001_2000.rds") +L2_2_gblup_prediction_all_2001_3000=readRDS(file="L2_2_gblup_prediction_all_2001_3000.rds") +L2_2_gblup_prediction_all_3001_4000=readRDS(file="L2_2_gblup_prediction_all_3001_4000.rds") +L2_2_gblup_prediction_all_4001_5000=readRDS(file="L2_2_gblup_prediction_all_4001_5000.rds") +L2_2_gblup_prediction_all_5001_6000=readRDS(file="L2_2_gblup_prediction_all_5001_6000.rds") +L2_2_gblup_prediction_all_6001_7000=readRDS(file="L2_2_gblup_prediction_all_6001_7000.rds") +L2_2_gblup_prediction_all_7001_8000=readRDS(file="L2_2_gblup_prediction_all_7001_8000.rds") +L2_2_gblup_prediction_all_8001_9000=readRDS(file="L2_2_gblup_prediction_all_8001_9000.rds") +L2_2_gblup_prediction_all_9001_10000=readRDS(file="L2_2_gblup_prediction_all_9001_10000.rds") +L2_2_gblup_prediction_all_10001_11000=readRDS(file="L2_2_gblup_prediction_all_10001_11000.rds") +L2_2_gblup_prediction_all_11001_12419=readRDS(file="L2_2_gblup_prediction_all_11001_12419.rds") +L2_2_gblup_prediction_all=c(L2_2_gblup_prediction_all_1_1000,L2_2_gblup_prediction_all_1001_2000,L2_2_gblup_prediction_all_2001_3000,L2_2_gblup_prediction_all_3001_4000,L2_2_gblup_prediction_all_4001_5000,L2_2_gblup_prediction_all_5001_6000,L2_2_gblup_prediction_all_6001_7000,L2_2_gblup_prediction_all_7001_8000,L2_2_gblup_prediction_all_8001_9000,L2_2_gblup_prediction_all_9001_10000,L2_2_gblup_prediction_all_10001_11000,L2_2_gblup_prediction_all_11001_12419) + +L2_2_gblup_variances_all_1_1000=readRDS(file="L2_2_gblup_variances_all_1_1000.rds") +L2_2_gblup_variances_all_1001_2000=readRDS(file="L2_2_gblup_variances_all_1001_2000.rds") +L2_2_gblup_variances_all_2001_3000=readRDS(file="L2_2_gblup_variances_all_2001_3000.rds") +L2_2_gblup_variances_all_3001_4000=readRDS(file="L2_2_gblup_variances_all_3001_4000.rds") +L2_2_gblup_variances_all_4001_5000=readRDS(file="L2_2_gblup_variances_all_4001_5000.rds") +L2_2_gblup_variances_all_5001_6000=readRDS(file="L2_2_gblup_variances_all_5001_6000.rds") +L2_2_gblup_variances_all_6001_7000=readRDS(file="L2_2_gblup_variances_all_6001_7000.rds") +L2_2_gblup_variances_all_7001_8000=readRDS(file="L2_2_gblup_variances_all_7001_8000.rds") +L2_2_gblup_variances_all_8001_9000=readRDS(file="L2_2_gblup_variances_all_8001_9000.rds") +L2_2_gblup_variances_all_9001_10000=readRDS(file="L2_2_gblup_variances_all_9001_10000.rds") +L2_2_gblup_variances_all_10001_11000=readRDS(file="L2_2_gblup_variances_all_10001_11000.rds") +L2_2_gblup_variances_all_11001_12419=readRDS(file="L2_2_gblup_variances_all_11001_12419.rds") +L2_2_gblup_variances_all=c(L2_2_gblup_variances_all_1_1000,L2_2_gblup_variances_all_1001_2000,L2_2_gblup_variances_all_2001_3000,L2_2_gblup_variances_all_3001_4000,L2_2_gblup_variances_all_4001_5000,L2_2_gblup_variances_all_5001_6000,L2_2_gblup_variances_all_6001_7000,L2_2_gblup_variances_all_7001_8000,L2_2_gblup_variances_all_8001_9000,L2_2_gblup_variances_all_9001_10000,L2_2_gblup_variances_all_10001_11000,L2_2_gblup_variances_all_11001_12419) + +saveRDS(L2_2_gblup_prediction_all,"L2_2_gblup_prediction_all.rds") +saveRDS(L2_2_gblup_variances_all,"L2_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +L2_2_gfblup_prediction_all_1_1000=readRDS(file="L2_2_gfblup_prediction_all_1_1000.rds") +L2_2_gfblup_prediction_all_1001_2000=readRDS(file="L2_2_gfblup_prediction_all_1001_2000.rds") +L2_2_gfblup_prediction_all_2001_3000=readRDS(file="L2_2_gfblup_prediction_all_2001_3000.rds") +L2_2_gfblup_prediction_all_3001_4000=readRDS(file="L2_2_gfblup_prediction_all_3001_4000.rds") +L2_2_gfblup_prediction_all_4001_5000=readRDS(file="L2_2_gfblup_prediction_all_4001_5000.rds") +L2_2_gfblup_prediction_all_5001_6000=readRDS(file="L2_2_gfblup_prediction_all_5001_6000.rds") +L2_2_gfblup_prediction_all_6001_7000=readRDS(file="L2_2_gfblup_prediction_all_6001_7000.rds") +L2_2_gfblup_prediction_all_7001_8000=readRDS(file="L2_2_gfblup_prediction_all_7001_8000.rds") +L2_2_gfblup_prediction_all_8001_9000=readRDS(file="L2_2_gfblup_prediction_all_8001_9000.rds") +L2_2_gfblup_prediction_all_9001_10000=readRDS(file="L2_2_gfblup_prediction_all_9001_10000.rds") +L2_2_gfblup_prediction_all_10001_11000=readRDS(file="L2_2_gfblup_prediction_all_10001_11000.rds") +L2_2_gfblup_prediction_all_11001_12419=readRDS(file="L2_2_gfblup_prediction_all_11001_12419.rds") + +L2_2_gfblup_variances_all_1_1000=readRDS(file="L2_2_gfblup_variances_all_1_1000.rds") +L2_2_gfblup_variances_all_1001_2000=readRDS(file="L2_2_gfblup_variances_all_1001_2000.rds") +L2_2_gfblup_variances_all_2001_3000=readRDS(file="L2_2_gfblup_variances_all_2001_3000.rds") +L2_2_gfblup_variances_all_3001_4000=readRDS(file="L2_2_gfblup_variances_all_3001_4000.rds") +L2_2_gfblup_variances_all_4001_5000=readRDS(file="L2_2_gfblup_variances_all_4001_5000.rds") +L2_2_gfblup_variances_all_5001_6000=readRDS(file="L2_2_gfblup_variances_all_5001_6000.rds") +L2_2_gfblup_variances_all_6001_7000=readRDS(file="L2_2_gfblup_variances_all_6001_7000.rds") +L2_2_gfblup_variances_all_7001_8000=readRDS(file="L2_2_gfblup_variances_all_7001_8000.rds") +L2_2_gfblup_variances_all_8001_9000=readRDS(file="L2_2_gfblup_variances_all_8001_9000.rds") +L2_2_gfblup_variances_all_9001_10000=readRDS(file="L2_2_gfblup_variances_all_9001_10000.rds") +L2_2_gfblup_variances_all_10001_11000=readRDS(file="L2_2_gfblup_variances_all_10001_11000.rds") +L2_2_gfblup_variances_all_11001_12419=readRDS(file="L2_2_gfblup_variances_all_11001_12419.rds") + +cycles=length(L2_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +L2_2_gfblup_variances_all=rep(list(list()),cycles) +L2_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_1_1000[[r]]) + L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_1001_2000[[r]]) + L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_2001_3000[[r]]) + L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_3001_4000[[r]]) + L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_4001_5000[[r]]) + L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_5001_6000[[r]]) + L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_6001_7000[[r]]) + L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_7001_8000[[r]]) + L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_8001_9000[[r]]) + L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_9001_10000[[r]]) + L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_10001_11000[[r]]) + L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_11001_12419[[r]]) + + L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_1_1000[[r]]) + L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_1001_2000[[r]]) + L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_2001_3000[[r]]) + L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_3001_4000[[r]]) + L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_4001_5000[[r]]) + L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_5001_6000[[r]]) + L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_6001_7000[[r]]) + L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_7001_8000[[r]]) + L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_8001_9000[[r]]) + L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_9001_10000[[r]]) + L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_10001_11000[[r]]) + L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(L2_2_gfblup_prediction_all,"L2_2_gfblup_prediction_all.rds") +saveRDS(L2_2_gfblup_variances_all,"L2_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +L2_3_gblup_prediction_all_1_1000=readRDS(file="L2_3_gblup_prediction_all_1_1000.rds") +L2_3_gblup_prediction_all_1001_2000=readRDS(file="L2_3_gblup_prediction_all_1001_2000.rds") +L2_3_gblup_prediction_all_2001_3000=readRDS(file="L2_3_gblup_prediction_all_2001_3000.rds") +L2_3_gblup_prediction_all_3001_4000=readRDS(file="L2_3_gblup_prediction_all_3001_4000.rds") +L2_3_gblup_prediction_all_4001_5000=readRDS(file="L2_3_gblup_prediction_all_4001_5000.rds") +L2_3_gblup_prediction_all_5001_6000=readRDS(file="L2_3_gblup_prediction_all_5001_6000.rds") +L2_3_gblup_prediction_all_6001_7000=readRDS(file="L2_3_gblup_prediction_all_6001_7000.rds") +L2_3_gblup_prediction_all_7001_8000=readRDS(file="L2_3_gblup_prediction_all_7001_8000.rds") +L2_3_gblup_prediction_all_8001_9000=readRDS(file="L2_3_gblup_prediction_all_8001_9000.rds") +L2_3_gblup_prediction_all_9001_10000=readRDS(file="L2_3_gblup_prediction_all_9001_10000.rds") +L2_3_gblup_prediction_all_10001_11000=readRDS(file="L2_3_gblup_prediction_all_10001_11000.rds") +L2_3_gblup_prediction_all_11001_12419=readRDS(file="L2_3_gblup_prediction_all_11001_12419.rds") +L2_3_gblup_prediction_all=c(L2_3_gblup_prediction_all_1_1000,L2_3_gblup_prediction_all_1001_2000,L2_3_gblup_prediction_all_2001_3000,L2_3_gblup_prediction_all_3001_4000,L2_3_gblup_prediction_all_4001_5000,L2_3_gblup_prediction_all_5001_6000,L2_3_gblup_prediction_all_6001_7000,L2_3_gblup_prediction_all_7001_8000,L2_3_gblup_prediction_all_8001_9000,L2_3_gblup_prediction_all_9001_10000,L2_3_gblup_prediction_all_10001_11000,L2_3_gblup_prediction_all_11001_12419) + +L2_3_gblup_variances_all_1_1000=readRDS(file="L2_3_gblup_variances_all_1_1000.rds") +L2_3_gblup_variances_all_1001_2000=readRDS(file="L2_3_gblup_variances_all_1001_2000.rds") +L2_3_gblup_variances_all_2001_3000=readRDS(file="L2_3_gblup_variances_all_2001_3000.rds") +L2_3_gblup_variances_all_3001_4000=readRDS(file="L2_3_gblup_variances_all_3001_4000.rds") +L2_3_gblup_variances_all_4001_5000=readRDS(file="L2_3_gblup_variances_all_4001_5000.rds") +L2_3_gblup_variances_all_5001_6000=readRDS(file="L2_3_gblup_variances_all_5001_6000.rds") +L2_3_gblup_variances_all_6001_7000=readRDS(file="L2_3_gblup_variances_all_6001_7000.rds") +L2_3_gblup_variances_all_7001_8000=readRDS(file="L2_3_gblup_variances_all_7001_8000.rds") +L2_3_gblup_variances_all_8001_9000=readRDS(file="L2_3_gblup_variances_all_8001_9000.rds") +L2_3_gblup_variances_all_9001_10000=readRDS(file="L2_3_gblup_variances_all_9001_10000.rds") +L2_3_gblup_variances_all_10001_11000=readRDS(file="L2_3_gblup_variances_all_10001_11000.rds") +L2_3_gblup_variances_all_11001_12419=readRDS(file="L2_3_gblup_variances_all_11001_12419.rds") +L2_3_gblup_variances_all=c(L2_3_gblup_variances_all_1_1000,L2_3_gblup_variances_all_1001_2000,L2_3_gblup_variances_all_2001_3000,L2_3_gblup_variances_all_3001_4000,L2_3_gblup_variances_all_4001_5000,L2_3_gblup_variances_all_5001_6000,L2_3_gblup_variances_all_6001_7000,L2_3_gblup_variances_all_7001_8000,L2_3_gblup_variances_all_8001_9000,L2_3_gblup_variances_all_9001_10000,L2_3_gblup_variances_all_10001_11000,L2_3_gblup_variances_all_11001_12419) + +saveRDS(L2_3_gblup_prediction_all,"L2_3_gblup_prediction_all.rds") +saveRDS(L2_3_gblup_variances_all,"L2_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +L2_3_gfblup_prediction_all_1_1000=readRDS(file="L2_3_gfblup_prediction_all_1_1000.rds") +L2_3_gfblup_prediction_all_1001_2000=readRDS(file="L2_3_gfblup_prediction_all_1001_2000.rds") +L2_3_gfblup_prediction_all_2001_3000=readRDS(file="L2_3_gfblup_prediction_all_2001_3000.rds") +L2_3_gfblup_prediction_all_3001_4000=readRDS(file="L2_3_gfblup_prediction_all_3001_4000.rds") +L2_3_gfblup_prediction_all_4001_5000=readRDS(file="L2_3_gfblup_prediction_all_4001_5000.rds") +L2_3_gfblup_prediction_all_5001_6000=readRDS(file="L2_3_gfblup_prediction_all_5001_6000.rds") +L2_3_gfblup_prediction_all_6001_7000=readRDS(file="L2_3_gfblup_prediction_all_6001_7000.rds") +L2_3_gfblup_prediction_all_7001_8000=readRDS(file="L2_3_gfblup_prediction_all_7001_8000.rds") +L2_3_gfblup_prediction_all_8001_9000=readRDS(file="L2_3_gfblup_prediction_all_8001_9000.rds") +L2_3_gfblup_prediction_all_9001_10000=readRDS(file="L2_3_gfblup_prediction_all_9001_10000.rds") +L2_3_gfblup_prediction_all_10001_11000=readRDS(file="L2_3_gfblup_prediction_all_10001_11000.rds") +L2_3_gfblup_prediction_all_11001_12419=readRDS(file="L2_3_gfblup_prediction_all_11001_12419.rds") + +L2_3_gfblup_variances_all_1_1000=readRDS(file="L2_3_gfblup_variances_all_1_1000.rds") +L2_3_gfblup_variances_all_1001_2000=readRDS(file="L2_3_gfblup_variances_all_1001_2000.rds") +L2_3_gfblup_variances_all_2001_3000=readRDS(file="L2_3_gfblup_variances_all_2001_3000.rds") +L2_3_gfblup_variances_all_3001_4000=readRDS(file="L2_3_gfblup_variances_all_3001_4000.rds") +L2_3_gfblup_variances_all_4001_5000=readRDS(file="L2_3_gfblup_variances_all_4001_5000.rds") +L2_3_gfblup_variances_all_5001_6000=readRDS(file="L2_3_gfblup_variances_all_5001_6000.rds") +L2_3_gfblup_variances_all_6001_7000=readRDS(file="L2_3_gfblup_variances_all_6001_7000.rds") +L2_3_gfblup_variances_all_7001_8000=readRDS(file="L2_3_gfblup_variances_all_7001_8000.rds") +L2_3_gfblup_variances_all_8001_9000=readRDS(file="L2_3_gfblup_variances_all_8001_9000.rds") +L2_3_gfblup_variances_all_9001_10000=readRDS(file="L2_3_gfblup_variances_all_9001_10000.rds") +L2_3_gfblup_variances_all_10001_11000=readRDS(file="L2_3_gfblup_variances_all_10001_11000.rds") +L2_3_gfblup_variances_all_11001_12419=readRDS(file="L2_3_gfblup_variances_all_11001_12419.rds") + +cycles=length(L2_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +L2_3_gfblup_variances_all=rep(list(list()),cycles) +L2_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_1_1000[[r]]) + L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_1001_2000[[r]]) + L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_2001_3000[[r]]) + L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_3001_4000[[r]]) + L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_4001_5000[[r]]) + L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_5001_6000[[r]]) + L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_6001_7000[[r]]) + L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_7001_8000[[r]]) + L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_8001_9000[[r]]) + L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_9001_10000[[r]]) + L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_10001_11000[[r]]) + L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_11001_12419[[r]]) + + L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_1_1000[[r]]) + L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_1001_2000[[r]]) + L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_2001_3000[[r]]) + L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_3001_4000[[r]]) + L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_4001_5000[[r]]) + L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_5001_6000[[r]]) + L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_6001_7000[[r]]) + L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_7001_8000[[r]]) + L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_8001_9000[[r]]) + L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_9001_10000[[r]]) + L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_10001_11000[[r]]) + L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(L2_3_gfblup_prediction_all,"L2_3_gfblup_prediction_all.rds") +saveRDS(L2_3_gfblup_variances_all,"L2_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H1_1_gblup_prediction_all_1_1000=readRDS(file="H1_1_gblup_prediction_all_1_1000.rds") +H1_1_gblup_prediction_all_1001_2000=readRDS(file="H1_1_gblup_prediction_all_1001_2000.rds") +H1_1_gblup_prediction_all_2001_3000=readRDS(file="H1_1_gblup_prediction_all_2001_3000.rds") +H1_1_gblup_prediction_all_3001_4000=readRDS(file="H1_1_gblup_prediction_all_3001_4000.rds") +H1_1_gblup_prediction_all_4001_5000=readRDS(file="H1_1_gblup_prediction_all_4001_5000.rds") +H1_1_gblup_prediction_all_5001_6000=readRDS(file="H1_1_gblup_prediction_all_5001_6000.rds") +H1_1_gblup_prediction_all_6001_7000=readRDS(file="H1_1_gblup_prediction_all_6001_7000.rds") +H1_1_gblup_prediction_all_7001_8000=readRDS(file="H1_1_gblup_prediction_all_7001_8000.rds") +H1_1_gblup_prediction_all_8001_9000=readRDS(file="H1_1_gblup_prediction_all_8001_9000.rds") +H1_1_gblup_prediction_all_9001_10000=readRDS(file="H1_1_gblup_prediction_all_9001_10000.rds") +H1_1_gblup_prediction_all_10001_11000=readRDS(file="H1_1_gblup_prediction_all_10001_11000.rds") +H1_1_gblup_prediction_all_11001_12419=readRDS(file="H1_1_gblup_prediction_all_11001_12419.rds") +H1_1_gblup_prediction_all=c(H1_1_gblup_prediction_all_1_1000,H1_1_gblup_prediction_all_1001_2000,H1_1_gblup_prediction_all_2001_3000,H1_1_gblup_prediction_all_3001_4000,H1_1_gblup_prediction_all_4001_5000,H1_1_gblup_prediction_all_5001_6000,H1_1_gblup_prediction_all_6001_7000,H1_1_gblup_prediction_all_7001_8000,H1_1_gblup_prediction_all_8001_9000,H1_1_gblup_prediction_all_9001_10000,H1_1_gblup_prediction_all_10001_11000,H1_1_gblup_prediction_all_11001_12419) + +H1_1_gblup_variances_all_1_1000=readRDS(file="H1_1_gblup_variances_all_1_1000.rds") +H1_1_gblup_variances_all_1001_2000=readRDS(file="H1_1_gblup_variances_all_1001_2000.rds") +H1_1_gblup_variances_all_2001_3000=readRDS(file="H1_1_gblup_variances_all_2001_3000.rds") +H1_1_gblup_variances_all_3001_4000=readRDS(file="H1_1_gblup_variances_all_3001_4000.rds") +H1_1_gblup_variances_all_4001_5000=readRDS(file="H1_1_gblup_variances_all_4001_5000.rds") +H1_1_gblup_variances_all_5001_6000=readRDS(file="H1_1_gblup_variances_all_5001_6000.rds") +H1_1_gblup_variances_all_6001_7000=readRDS(file="H1_1_gblup_variances_all_6001_7000.rds") +H1_1_gblup_variances_all_7001_8000=readRDS(file="H1_1_gblup_variances_all_7001_8000.rds") +H1_1_gblup_variances_all_8001_9000=readRDS(file="H1_1_gblup_variances_all_8001_9000.rds") +H1_1_gblup_variances_all_9001_10000=readRDS(file="H1_1_gblup_variances_all_9001_10000.rds") +H1_1_gblup_variances_all_10001_11000=readRDS(file="H1_1_gblup_variances_all_10001_11000.rds") +H1_1_gblup_variances_all_11001_12419=readRDS(file="H1_1_gblup_variances_all_11001_12419.rds") +H1_1_gblup_variances_all=c(H1_1_gblup_variances_all_1_1000,H1_1_gblup_variances_all_1001_2000,H1_1_gblup_variances_all_2001_3000,H1_1_gblup_variances_all_3001_4000,H1_1_gblup_variances_all_4001_5000,H1_1_gblup_variances_all_5001_6000,H1_1_gblup_variances_all_6001_7000,H1_1_gblup_variances_all_7001_8000,H1_1_gblup_variances_all_8001_9000,H1_1_gblup_variances_all_9001_10000,H1_1_gblup_variances_all_10001_11000,H1_1_gblup_variances_all_11001_12419) + +saveRDS(H1_1_gblup_prediction_all,"H1_1_gblup_prediction_all.rds") +saveRDS(H1_1_gblup_variances_all,"H1_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H1_1_gfblup_prediction_all_1_1000=readRDS(file="H1_1_gfblup_prediction_all_1_1000.rds") +H1_1_gfblup_prediction_all_1001_2000=readRDS(file="H1_1_gfblup_prediction_all_1001_2000.rds") +H1_1_gfblup_prediction_all_2001_3000=readRDS(file="H1_1_gfblup_prediction_all_2001_3000.rds") +H1_1_gfblup_prediction_all_3001_4000=readRDS(file="H1_1_gfblup_prediction_all_3001_4000.rds") +H1_1_gfblup_prediction_all_4001_5000=readRDS(file="H1_1_gfblup_prediction_all_4001_5000.rds") +H1_1_gfblup_prediction_all_5001_6000=readRDS(file="H1_1_gfblup_prediction_all_5001_6000.rds") +H1_1_gfblup_prediction_all_6001_7000=readRDS(file="H1_1_gfblup_prediction_all_6001_7000.rds") +H1_1_gfblup_prediction_all_7001_8000=readRDS(file="H1_1_gfblup_prediction_all_7001_8000.rds") +H1_1_gfblup_prediction_all_8001_9000=readRDS(file="H1_1_gfblup_prediction_all_8001_9000.rds") +H1_1_gfblup_prediction_all_9001_10000=readRDS(file="H1_1_gfblup_prediction_all_9001_10000.rds") +H1_1_gfblup_prediction_all_10001_11000=readRDS(file="H1_1_gfblup_prediction_all_10001_11000.rds") +H1_1_gfblup_prediction_all_11001_12419=readRDS(file="H1_1_gfblup_prediction_all_11001_12419.rds") + +H1_1_gfblup_variances_all_1_1000=readRDS(file="H1_1_gfblup_variances_all_1_1000.rds") +H1_1_gfblup_variances_all_1001_2000=readRDS(file="H1_1_gfblup_variances_all_1001_2000.rds") +H1_1_gfblup_variances_all_2001_3000=readRDS(file="H1_1_gfblup_variances_all_2001_3000.rds") +H1_1_gfblup_variances_all_3001_4000=readRDS(file="H1_1_gfblup_variances_all_3001_4000.rds") +H1_1_gfblup_variances_all_4001_5000=readRDS(file="H1_1_gfblup_variances_all_4001_5000.rds") +H1_1_gfblup_variances_all_5001_6000=readRDS(file="H1_1_gfblup_variances_all_5001_6000.rds") +H1_1_gfblup_variances_all_6001_7000=readRDS(file="H1_1_gfblup_variances_all_6001_7000.rds") +H1_1_gfblup_variances_all_7001_8000=readRDS(file="H1_1_gfblup_variances_all_7001_8000.rds") +H1_1_gfblup_variances_all_8001_9000=readRDS(file="H1_1_gfblup_variances_all_8001_9000.rds") +H1_1_gfblup_variances_all_9001_10000=readRDS(file="H1_1_gfblup_variances_all_9001_10000.rds") +H1_1_gfblup_variances_all_10001_11000=readRDS(file="H1_1_gfblup_variances_all_10001_11000.rds") +H1_1_gfblup_variances_all_11001_12419=readRDS(file="H1_1_gfblup_variances_all_11001_12419.rds") + +cycles=length(H1_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H1_1_gfblup_variances_all=rep(list(list()),cycles) +H1_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_1_1000[[r]]) + H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_1001_2000[[r]]) + H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_2001_3000[[r]]) + H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_3001_4000[[r]]) + H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_4001_5000[[r]]) + H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_5001_6000[[r]]) + H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_6001_7000[[r]]) + H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_7001_8000[[r]]) + H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_8001_9000[[r]]) + H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_9001_10000[[r]]) + H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_10001_11000[[r]]) + H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_11001_12419[[r]]) + + H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_1_1000[[r]]) + H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_1001_2000[[r]]) + H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_2001_3000[[r]]) + H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_3001_4000[[r]]) + H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_4001_5000[[r]]) + H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_5001_6000[[r]]) + H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_6001_7000[[r]]) + H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_7001_8000[[r]]) + H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_8001_9000[[r]]) + H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_9001_10000[[r]]) + H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_10001_11000[[r]]) + H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(H1_1_gfblup_prediction_all,"H1_1_gfblup_prediction_all.rds") +saveRDS(H1_1_gfblup_variances_all,"H1_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H1_2_gblup_prediction_all_1_1000=readRDS(file="H1_2_gblup_prediction_all_1_1000.rds") +H1_2_gblup_prediction_all_1001_2000=readRDS(file="H1_2_gblup_prediction_all_1001_2000.rds") +H1_2_gblup_prediction_all_2001_3000=readRDS(file="H1_2_gblup_prediction_all_2001_3000.rds") +H1_2_gblup_prediction_all_3001_4000=readRDS(file="H1_2_gblup_prediction_all_3001_4000.rds") +H1_2_gblup_prediction_all_4001_5000=readRDS(file="H1_2_gblup_prediction_all_4001_5000.rds") +H1_2_gblup_prediction_all_5001_6000=readRDS(file="H1_2_gblup_prediction_all_5001_6000.rds") +H1_2_gblup_prediction_all_6001_7000=readRDS(file="H1_2_gblup_prediction_all_6001_7000.rds") +H1_2_gblup_prediction_all_7001_8000=readRDS(file="H1_2_gblup_prediction_all_7001_8000.rds") +H1_2_gblup_prediction_all_8001_9000=readRDS(file="H1_2_gblup_prediction_all_8001_9000.rds") +H1_2_gblup_prediction_all_9001_10000=readRDS(file="H1_2_gblup_prediction_all_9001_10000.rds") +H1_2_gblup_prediction_all_10001_11000=readRDS(file="H1_2_gblup_prediction_all_10001_11000.rds") +H1_2_gblup_prediction_all_11001_12419=readRDS(file="H1_2_gblup_prediction_all_11001_12419.rds") +H1_2_gblup_prediction_all=c(H1_2_gblup_prediction_all_1_1000,H1_2_gblup_prediction_all_1001_2000,H1_2_gblup_prediction_all_2001_3000,H1_2_gblup_prediction_all_3001_4000,H1_2_gblup_prediction_all_4001_5000,H1_2_gblup_prediction_all_5001_6000,H1_2_gblup_prediction_all_6001_7000,H1_2_gblup_prediction_all_7001_8000,H1_2_gblup_prediction_all_8001_9000,H1_2_gblup_prediction_all_9001_10000,H1_2_gblup_prediction_all_10001_11000,H1_2_gblup_prediction_all_11001_12419) + +H1_2_gblup_variances_all_1_1000=readRDS(file="H1_2_gblup_variances_all_1_1000.rds") +H1_2_gblup_variances_all_1001_2000=readRDS(file="H1_2_gblup_variances_all_1001_2000.rds") +H1_2_gblup_variances_all_2001_3000=readRDS(file="H1_2_gblup_variances_all_2001_3000.rds") +H1_2_gblup_variances_all_3001_4000=readRDS(file="H1_2_gblup_variances_all_3001_4000.rds") +H1_2_gblup_variances_all_4001_5000=readRDS(file="H1_2_gblup_variances_all_4001_5000.rds") +H1_2_gblup_variances_all_5001_6000=readRDS(file="H1_2_gblup_variances_all_5001_6000.rds") +H1_2_gblup_variances_all_6001_7000=readRDS(file="H1_2_gblup_variances_all_6001_7000.rds") +H1_2_gblup_variances_all_7001_8000=readRDS(file="H1_2_gblup_variances_all_7001_8000.rds") +H1_2_gblup_variances_all_8001_9000=readRDS(file="H1_2_gblup_variances_all_8001_9000.rds") +H1_2_gblup_variances_all_9001_10000=readRDS(file="H1_2_gblup_variances_all_9001_10000.rds") +H1_2_gblup_variances_all_10001_11000=readRDS(file="H1_2_gblup_variances_all_10001_11000.rds") +H1_2_gblup_variances_all_11001_12419=readRDS(file="H1_2_gblup_variances_all_11001_12419.rds") +H1_2_gblup_variances_all=c(H1_2_gblup_variances_all_1_1000,H1_2_gblup_variances_all_1001_2000,H1_2_gblup_variances_all_2001_3000,H1_2_gblup_variances_all_3001_4000,H1_2_gblup_variances_all_4001_5000,H1_2_gblup_variances_all_5001_6000,H1_2_gblup_variances_all_6001_7000,H1_2_gblup_variances_all_7001_8000,H1_2_gblup_variances_all_8001_9000,H1_2_gblup_variances_all_9001_10000,H1_2_gblup_variances_all_10001_11000,H1_2_gblup_variances_all_11001_12419) + +saveRDS(H1_2_gblup_prediction_all,"H1_2_gblup_prediction_all.rds") +saveRDS(H1_2_gblup_variances_all,"H1_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H1_2_gfblup_prediction_all_1_1000=readRDS(file="H1_2_gfblup_prediction_all_1_1000.rds") +H1_2_gfblup_prediction_all_1001_2000=readRDS(file="H1_2_gfblup_prediction_all_1001_2000.rds") +H1_2_gfblup_prediction_all_2001_3000=readRDS(file="H1_2_gfblup_prediction_all_2001_3000.rds") +H1_2_gfblup_prediction_all_3001_4000=readRDS(file="H1_2_gfblup_prediction_all_3001_4000.rds") +H1_2_gfblup_prediction_all_4001_5000=readRDS(file="H1_2_gfblup_prediction_all_4001_5000.rds") +H1_2_gfblup_prediction_all_5001_6000=readRDS(file="H1_2_gfblup_prediction_all_5001_6000.rds") +H1_2_gfblup_prediction_all_6001_7000=readRDS(file="H1_2_gfblup_prediction_all_6001_7000.rds") +H1_2_gfblup_prediction_all_7001_8000=readRDS(file="H1_2_gfblup_prediction_all_7001_8000.rds") +H1_2_gfblup_prediction_all_8001_9000=readRDS(file="H1_2_gfblup_prediction_all_8001_9000.rds") +H1_2_gfblup_prediction_all_9001_10000=readRDS(file="H1_2_gfblup_prediction_all_9001_10000.rds") +H1_2_gfblup_prediction_all_10001_11000=readRDS(file="H1_2_gfblup_prediction_all_10001_11000.rds") +H1_2_gfblup_prediction_all_11001_12419=readRDS(file="H1_2_gfblup_prediction_all_11001_12419.rds") + +H1_2_gfblup_variances_all_1_1000=readRDS(file="H1_2_gfblup_variances_all_1_1000.rds") +H1_2_gfblup_variances_all_1001_2000=readRDS(file="H1_2_gfblup_variances_all_1001_2000.rds") +H1_2_gfblup_variances_all_2001_3000=readRDS(file="H1_2_gfblup_variances_all_2001_3000.rds") +H1_2_gfblup_variances_all_3001_4000=readRDS(file="H1_2_gfblup_variances_all_3001_4000.rds") +H1_2_gfblup_variances_all_4001_5000=readRDS(file="H1_2_gfblup_variances_all_4001_5000.rds") +H1_2_gfblup_variances_all_5001_6000=readRDS(file="H1_2_gfblup_variances_all_5001_6000.rds") +H1_2_gfblup_variances_all_6001_7000=readRDS(file="H1_2_gfblup_variances_all_6001_7000.rds") +H1_2_gfblup_variances_all_7001_8000=readRDS(file="H1_2_gfblup_variances_all_7001_8000.rds") +H1_2_gfblup_variances_all_8001_9000=readRDS(file="H1_2_gfblup_variances_all_8001_9000.rds") +H1_2_gfblup_variances_all_9001_10000=readRDS(file="H1_2_gfblup_variances_all_9001_10000.rds") +H1_2_gfblup_variances_all_10001_11000=readRDS(file="H1_2_gfblup_variances_all_10001_11000.rds") +H1_2_gfblup_variances_all_11001_12419=readRDS(file="H1_2_gfblup_variances_all_11001_12419.rds") + +cycles=length(H1_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H1_2_gfblup_variances_all=rep(list(list()),cycles) +H1_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_1_1000[[r]]) + H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_1001_2000[[r]]) + H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_2001_3000[[r]]) + H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_3001_4000[[r]]) + H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_4001_5000[[r]]) + H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_5001_6000[[r]]) + H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_6001_7000[[r]]) + H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_7001_8000[[r]]) + H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_8001_9000[[r]]) + H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_9001_10000[[r]]) + H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_10001_11000[[r]]) + H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_11001_12419[[r]]) + + H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_1_1000[[r]]) + H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_1001_2000[[r]]) + H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_2001_3000[[r]]) + H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_3001_4000[[r]]) + H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_4001_5000[[r]]) + H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_5001_6000[[r]]) + H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_6001_7000[[r]]) + H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_7001_8000[[r]]) + H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_8001_9000[[r]]) + H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_9001_10000[[r]]) + H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_10001_11000[[r]]) + H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(H1_2_gfblup_prediction_all,"H1_2_gfblup_prediction_all.rds") +saveRDS(H1_2_gfblup_variances_all,"H1_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H1_3_gblup_prediction_all_1_1000=readRDS(file="H1_3_gblup_prediction_all_1_1000.rds") +H1_3_gblup_prediction_all_1001_2000=readRDS(file="H1_3_gblup_prediction_all_1001_2000.rds") +H1_3_gblup_prediction_all_2001_3000=readRDS(file="H1_3_gblup_prediction_all_2001_3000.rds") +H1_3_gblup_prediction_all_3001_4000=readRDS(file="H1_3_gblup_prediction_all_3001_4000.rds") +H1_3_gblup_prediction_all_4001_5000=readRDS(file="H1_3_gblup_prediction_all_4001_5000.rds") +H1_3_gblup_prediction_all_5001_6000=readRDS(file="H1_3_gblup_prediction_all_5001_6000.rds") +H1_3_gblup_prediction_all_6001_7000=readRDS(file="H1_3_gblup_prediction_all_6001_7000.rds") +H1_3_gblup_prediction_all_7001_8000=readRDS(file="H1_3_gblup_prediction_all_7001_8000.rds") +H1_3_gblup_prediction_all_8001_9000=readRDS(file="H1_3_gblup_prediction_all_8001_9000.rds") +H1_3_gblup_prediction_all_9001_10000=readRDS(file="H1_3_gblup_prediction_all_9001_10000.rds") +H1_3_gblup_prediction_all_10001_11000=readRDS(file="H1_3_gblup_prediction_all_10001_11000.rds") +H1_3_gblup_prediction_all_11001_12419=readRDS(file="H1_3_gblup_prediction_all_11001_12419.rds") +H1_3_gblup_prediction_all=c(H1_3_gblup_prediction_all_1_1000,H1_3_gblup_prediction_all_1001_2000,H1_3_gblup_prediction_all_2001_3000,H1_3_gblup_prediction_all_3001_4000,H1_3_gblup_prediction_all_4001_5000,H1_3_gblup_prediction_all_5001_6000,H1_3_gblup_prediction_all_6001_7000,H1_3_gblup_prediction_all_7001_8000,H1_3_gblup_prediction_all_8001_9000,H1_3_gblup_prediction_all_9001_10000,H1_3_gblup_prediction_all_10001_11000,H1_3_gblup_prediction_all_11001_12419) + +H1_3_gblup_variances_all_1_1000=readRDS(file="H1_3_gblup_variances_all_1_1000.rds") +H1_3_gblup_variances_all_1001_2000=readRDS(file="H1_3_gblup_variances_all_1001_2000.rds") +H1_3_gblup_variances_all_2001_3000=readRDS(file="H1_3_gblup_variances_all_2001_3000.rds") +H1_3_gblup_variances_all_3001_4000=readRDS(file="H1_3_gblup_variances_all_3001_4000.rds") +H1_3_gblup_variances_all_4001_5000=readRDS(file="H1_3_gblup_variances_all_4001_5000.rds") +H1_3_gblup_variances_all_5001_6000=readRDS(file="H1_3_gblup_variances_all_5001_6000.rds") +H1_3_gblup_variances_all_6001_7000=readRDS(file="H1_3_gblup_variances_all_6001_7000.rds") +H1_3_gblup_variances_all_7001_8000=readRDS(file="H1_3_gblup_variances_all_7001_8000.rds") +H1_3_gblup_variances_all_8001_9000=readRDS(file="H1_3_gblup_variances_all_8001_9000.rds") +H1_3_gblup_variances_all_9001_10000=readRDS(file="H1_3_gblup_variances_all_9001_10000.rds") +H1_3_gblup_variances_all_10001_11000=readRDS(file="H1_3_gblup_variances_all_10001_11000.rds") +H1_3_gblup_variances_all_11001_12419=readRDS(file="H1_3_gblup_variances_all_11001_12419.rds") +H1_3_gblup_variances_all=c(H1_3_gblup_variances_all_1_1000,H1_3_gblup_variances_all_1001_2000,H1_3_gblup_variances_all_2001_3000,H1_3_gblup_variances_all_3001_4000,H1_3_gblup_variances_all_4001_5000,H1_3_gblup_variances_all_5001_6000,H1_3_gblup_variances_all_6001_7000,H1_3_gblup_variances_all_7001_8000,H1_3_gblup_variances_all_8001_9000,H1_3_gblup_variances_all_9001_10000,H1_3_gblup_variances_all_10001_11000,H1_3_gblup_variances_all_11001_12419) + +saveRDS(H1_3_gblup_prediction_all,"H1_3_gblup_prediction_all.rds") +saveRDS(H1_3_gblup_variances_all,"H1_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H1_3_gfblup_prediction_all_1_1000=readRDS(file="H1_3_gfblup_prediction_all_1_1000.rds") +H1_3_gfblup_prediction_all_1001_2000=readRDS(file="H1_3_gfblup_prediction_all_1001_2000.rds") +H1_3_gfblup_prediction_all_2001_3000=readRDS(file="H1_3_gfblup_prediction_all_2001_3000.rds") +H1_3_gfblup_prediction_all_3001_4000=readRDS(file="H1_3_gfblup_prediction_all_3001_4000.rds") +H1_3_gfblup_prediction_all_4001_5000=readRDS(file="H1_3_gfblup_prediction_all_4001_5000.rds") +H1_3_gfblup_prediction_all_5001_6000=readRDS(file="H1_3_gfblup_prediction_all_5001_6000.rds") +H1_3_gfblup_prediction_all_6001_7000=readRDS(file="H1_3_gfblup_prediction_all_6001_7000.rds") +H1_3_gfblup_prediction_all_7001_8000=readRDS(file="H1_3_gfblup_prediction_all_7001_8000.rds") +H1_3_gfblup_prediction_all_8001_9000=readRDS(file="H1_3_gfblup_prediction_all_8001_9000.rds") +H1_3_gfblup_prediction_all_9001_10000=readRDS(file="H1_3_gfblup_prediction_all_9001_10000.rds") +H1_3_gfblup_prediction_all_10001_11000=readRDS(file="H1_3_gfblup_prediction_all_10001_11000.rds") +H1_3_gfblup_prediction_all_11001_12419=readRDS(file="H1_3_gfblup_prediction_all_11001_12419.rds") + +H1_3_gfblup_variances_all_1_1000=readRDS(file="H1_3_gfblup_variances_all_1_1000.rds") +H1_3_gfblup_variances_all_1001_2000=readRDS(file="H1_3_gfblup_variances_all_1001_2000.rds") +H1_3_gfblup_variances_all_2001_3000=readRDS(file="H1_3_gfblup_variances_all_2001_3000.rds") +H1_3_gfblup_variances_all_3001_4000=readRDS(file="H1_3_gfblup_variances_all_3001_4000.rds") +H1_3_gfblup_variances_all_4001_5000=readRDS(file="H1_3_gfblup_variances_all_4001_5000.rds") +H1_3_gfblup_variances_all_5001_6000=readRDS(file="H1_3_gfblup_variances_all_5001_6000.rds") +H1_3_gfblup_variances_all_6001_7000=readRDS(file="H1_3_gfblup_variances_all_6001_7000.rds") +H1_3_gfblup_variances_all_7001_8000=readRDS(file="H1_3_gfblup_variances_all_7001_8000.rds") +H1_3_gfblup_variances_all_8001_9000=readRDS(file="H1_3_gfblup_variances_all_8001_9000.rds") +H1_3_gfblup_variances_all_9001_10000=readRDS(file="H1_3_gfblup_variances_all_9001_10000.rds") +H1_3_gfblup_variances_all_10001_11000=readRDS(file="H1_3_gfblup_variances_all_10001_11000.rds") +H1_3_gfblup_variances_all_11001_12419=readRDS(file="H1_3_gfblup_variances_all_11001_12419.rds") + +cycles=length(H1_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H1_3_gfblup_variances_all=rep(list(list()),cycles) +H1_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_1_1000[[r]]) + H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_1001_2000[[r]]) + H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_2001_3000[[r]]) + H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_3001_4000[[r]]) + H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_4001_5000[[r]]) + H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_5001_6000[[r]]) + H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_6001_7000[[r]]) + H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_7001_8000[[r]]) + H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_8001_9000[[r]]) + H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_9001_10000[[r]]) + H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_10001_11000[[r]]) + H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_11001_12419[[r]]) + + H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_1_1000[[r]]) + H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_1001_2000[[r]]) + H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_2001_3000[[r]]) + H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_3001_4000[[r]]) + H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_4001_5000[[r]]) + H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_5001_6000[[r]]) + H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_6001_7000[[r]]) + H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_7001_8000[[r]]) + H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_8001_9000[[r]]) + H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_9001_10000[[r]]) + H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_10001_11000[[r]]) + H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(H1_3_gfblup_prediction_all,"H1_3_gfblup_prediction_all.rds") +saveRDS(H1_3_gfblup_variances_all,"H1_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H2_1_gblup_prediction_all_1_1000=readRDS(file="H2_1_gblup_prediction_all_1_1000.rds") +H2_1_gblup_prediction_all_1001_2000=readRDS(file="H2_1_gblup_prediction_all_1001_2000.rds") +H2_1_gblup_prediction_all_2001_3000=readRDS(file="H2_1_gblup_prediction_all_2001_3000.rds") +H2_1_gblup_prediction_all_3001_4000=readRDS(file="H2_1_gblup_prediction_all_3001_4000.rds") +H2_1_gblup_prediction_all_4001_5000=readRDS(file="H2_1_gblup_prediction_all_4001_5000.rds") +H2_1_gblup_prediction_all_5001_6000=readRDS(file="H2_1_gblup_prediction_all_5001_6000.rds") +H2_1_gblup_prediction_all_6001_7000=readRDS(file="H2_1_gblup_prediction_all_6001_7000.rds") +H2_1_gblup_prediction_all_7001_8000=readRDS(file="H2_1_gblup_prediction_all_7001_8000.rds") +H2_1_gblup_prediction_all_8001_9000=readRDS(file="H2_1_gblup_prediction_all_8001_9000.rds") +H2_1_gblup_prediction_all_9001_10000=readRDS(file="H2_1_gblup_prediction_all_9001_10000.rds") +H2_1_gblup_prediction_all_10001_11000=readRDS(file="H2_1_gblup_prediction_all_10001_11000.rds") +H2_1_gblup_prediction_all_11001_12419=readRDS(file="H2_1_gblup_prediction_all_11001_12419.rds") +H2_1_gblup_prediction_all=c(H2_1_gblup_prediction_all_1_1000,H2_1_gblup_prediction_all_1001_2000,H2_1_gblup_prediction_all_2001_3000,H2_1_gblup_prediction_all_3001_4000,H2_1_gblup_prediction_all_4001_5000,H2_1_gblup_prediction_all_5001_6000,H2_1_gblup_prediction_all_6001_7000,H2_1_gblup_prediction_all_7001_8000,H2_1_gblup_prediction_all_8001_9000,H2_1_gblup_prediction_all_9001_10000,H2_1_gblup_prediction_all_10001_11000,H2_1_gblup_prediction_all_11001_12419) + +H2_1_gblup_variances_all_1_1000=readRDS(file="H2_1_gblup_variances_all_1_1000.rds") +H2_1_gblup_variances_all_1001_2000=readRDS(file="H2_1_gblup_variances_all_1001_2000.rds") +H2_1_gblup_variances_all_2001_3000=readRDS(file="H2_1_gblup_variances_all_2001_3000.rds") +H2_1_gblup_variances_all_3001_4000=readRDS(file="H2_1_gblup_variances_all_3001_4000.rds") +H2_1_gblup_variances_all_4001_5000=readRDS(file="H2_1_gblup_variances_all_4001_5000.rds") +H2_1_gblup_variances_all_5001_6000=readRDS(file="H2_1_gblup_variances_all_5001_6000.rds") +H2_1_gblup_variances_all_6001_7000=readRDS(file="H2_1_gblup_variances_all_6001_7000.rds") +H2_1_gblup_variances_all_7001_8000=readRDS(file="H2_1_gblup_variances_all_7001_8000.rds") +H2_1_gblup_variances_all_8001_9000=readRDS(file="H2_1_gblup_variances_all_8001_9000.rds") +H2_1_gblup_variances_all_9001_10000=readRDS(file="H2_1_gblup_variances_all_9001_10000.rds") +H2_1_gblup_variances_all_10001_11000=readRDS(file="H2_1_gblup_variances_all_10001_11000.rds") +H2_1_gblup_variances_all_11001_12419=readRDS(file="H2_1_gblup_variances_all_11001_12419.rds") +H2_1_gblup_variances_all=c(H2_1_gblup_variances_all_1_1000,H2_1_gblup_variances_all_1001_2000,H2_1_gblup_variances_all_2001_3000,H2_1_gblup_variances_all_3001_4000,H2_1_gblup_variances_all_4001_5000,H2_1_gblup_variances_all_5001_6000,H2_1_gblup_variances_all_6001_7000,H2_1_gblup_variances_all_7001_8000,H2_1_gblup_variances_all_8001_9000,H2_1_gblup_variances_all_9001_10000,H2_1_gblup_variances_all_10001_11000,H2_1_gblup_variances_all_11001_12419) + +saveRDS(H2_1_gblup_prediction_all,"H2_1_gblup_prediction_all.rds") +saveRDS(H2_1_gblup_variances_all,"H2_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H2_1_gfblup_prediction_all_1_1000=readRDS(file="H2_1_gfblup_prediction_all_1_1000.rds") +H2_1_gfblup_prediction_all_1001_2000=readRDS(file="H2_1_gfblup_prediction_all_1001_2000.rds") +H2_1_gfblup_prediction_all_2001_3000=readRDS(file="H2_1_gfblup_prediction_all_2001_3000.rds") +H2_1_gfblup_prediction_all_3001_4000=readRDS(file="H2_1_gfblup_prediction_all_3001_4000.rds") +H2_1_gfblup_prediction_all_4001_5000=readRDS(file="H2_1_gfblup_prediction_all_4001_5000.rds") +H2_1_gfblup_prediction_all_5001_6000=readRDS(file="H2_1_gfblup_prediction_all_5001_6000.rds") +H2_1_gfblup_prediction_all_6001_7000=readRDS(file="H2_1_gfblup_prediction_all_6001_7000.rds") +H2_1_gfblup_prediction_all_7001_8000=readRDS(file="H2_1_gfblup_prediction_all_7001_8000.rds") +H2_1_gfblup_prediction_all_8001_9000=readRDS(file="H2_1_gfblup_prediction_all_8001_9000.rds") +H2_1_gfblup_prediction_all_9001_10000=readRDS(file="H2_1_gfblup_prediction_all_9001_10000.rds") +H2_1_gfblup_prediction_all_10001_11000=readRDS(file="H2_1_gfblup_prediction_all_10001_11000.rds") +H2_1_gfblup_prediction_all_11001_12419=readRDS(file="H2_1_gfblup_prediction_all_11001_12419.rds") + +H2_1_gfblup_variances_all_1_1000=readRDS(file="H2_1_gfblup_variances_all_1_1000.rds") +H2_1_gfblup_variances_all_1001_2000=readRDS(file="H2_1_gfblup_variances_all_1001_2000.rds") +H2_1_gfblup_variances_all_2001_3000=readRDS(file="H2_1_gfblup_variances_all_2001_3000.rds") +H2_1_gfblup_variances_all_3001_4000=readRDS(file="H2_1_gfblup_variances_all_3001_4000.rds") +H2_1_gfblup_variances_all_4001_5000=readRDS(file="H2_1_gfblup_variances_all_4001_5000.rds") +H2_1_gfblup_variances_all_5001_6000=readRDS(file="H2_1_gfblup_variances_all_5001_6000.rds") +H2_1_gfblup_variances_all_6001_7000=readRDS(file="H2_1_gfblup_variances_all_6001_7000.rds") +H2_1_gfblup_variances_all_7001_8000=readRDS(file="H2_1_gfblup_variances_all_7001_8000.rds") +H2_1_gfblup_variances_all_8001_9000=readRDS(file="H2_1_gfblup_variances_all_8001_9000.rds") +H2_1_gfblup_variances_all_9001_10000=readRDS(file="H2_1_gfblup_variances_all_9001_10000.rds") +H2_1_gfblup_variances_all_10001_11000=readRDS(file="H2_1_gfblup_variances_all_10001_11000.rds") +H2_1_gfblup_variances_all_11001_12419=readRDS(file="H2_1_gfblup_variances_all_11001_12419.rds") + +cycles=length(H2_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H2_1_gfblup_variances_all=rep(list(list()),cycles) +H2_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_1_1000[[r]]) + H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_1001_2000[[r]]) + H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_2001_3000[[r]]) + H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_3001_4000[[r]]) + H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_4001_5000[[r]]) + H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_5001_6000[[r]]) + H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_6001_7000[[r]]) + H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_7001_8000[[r]]) + H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_8001_9000[[r]]) + H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_9001_10000[[r]]) + H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_10001_11000[[r]]) + H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_11001_12419[[r]]) + + H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_1_1000[[r]]) + H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_1001_2000[[r]]) + H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_2001_3000[[r]]) + H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_3001_4000[[r]]) + H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_4001_5000[[r]]) + H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_5001_6000[[r]]) + H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_6001_7000[[r]]) + H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_7001_8000[[r]]) + H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_8001_9000[[r]]) + H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_9001_10000[[r]]) + H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_10001_11000[[r]]) + H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(H2_1_gfblup_prediction_all,"H2_1_gfblup_prediction_all.rds") +saveRDS(H2_1_gfblup_variances_all,"H2_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H2_2_gblup_prediction_all_1_1000=readRDS(file="H2_2_gblup_prediction_all_1_1000.rds") +H2_2_gblup_prediction_all_1001_2000=readRDS(file="H2_2_gblup_prediction_all_1001_2000.rds") +H2_2_gblup_prediction_all_2001_3000=readRDS(file="H2_2_gblup_prediction_all_2001_3000.rds") +H2_2_gblup_prediction_all_3001_4000=readRDS(file="H2_2_gblup_prediction_all_3001_4000.rds") +H2_2_gblup_prediction_all_4001_5000=readRDS(file="H2_2_gblup_prediction_all_4001_5000.rds") +H2_2_gblup_prediction_all_5001_6000=readRDS(file="H2_2_gblup_prediction_all_5001_6000.rds") +H2_2_gblup_prediction_all_6001_7000=readRDS(file="H2_2_gblup_prediction_all_6001_7000.rds") +H2_2_gblup_prediction_all_7001_8000=readRDS(file="H2_2_gblup_prediction_all_7001_8000.rds") +H2_2_gblup_prediction_all_8001_9000=readRDS(file="H2_2_gblup_prediction_all_8001_9000.rds") +H2_2_gblup_prediction_all_9001_10000=readRDS(file="H2_2_gblup_prediction_all_9001_10000.rds") +H2_2_gblup_prediction_all_10001_11000=readRDS(file="H2_2_gblup_prediction_all_10001_11000.rds") +H2_2_gblup_prediction_all_11001_12419=readRDS(file="H2_2_gblup_prediction_all_11001_12419.rds") +H2_2_gblup_prediction_all=c(H2_2_gblup_prediction_all_1_1000,H2_2_gblup_prediction_all_1001_2000,H2_2_gblup_prediction_all_2001_3000,H2_2_gblup_prediction_all_3001_4000,H2_2_gblup_prediction_all_4001_5000,H2_2_gblup_prediction_all_5001_6000,H2_2_gblup_prediction_all_6001_7000,H2_2_gblup_prediction_all_7001_8000,H2_2_gblup_prediction_all_8001_9000,H2_2_gblup_prediction_all_9001_10000,H2_2_gblup_prediction_all_10001_11000,H2_2_gblup_prediction_all_11001_12419) + +H2_2_gblup_variances_all_1_1000=readRDS(file="H2_2_gblup_variances_all_1_1000.rds") +H2_2_gblup_variances_all_1001_2000=readRDS(file="H2_2_gblup_variances_all_1001_2000.rds") +H2_2_gblup_variances_all_2001_3000=readRDS(file="H2_2_gblup_variances_all_2001_3000.rds") +H2_2_gblup_variances_all_3001_4000=readRDS(file="H2_2_gblup_variances_all_3001_4000.rds") +H2_2_gblup_variances_all_4001_5000=readRDS(file="H2_2_gblup_variances_all_4001_5000.rds") +H2_2_gblup_variances_all_5001_6000=readRDS(file="H2_2_gblup_variances_all_5001_6000.rds") +H2_2_gblup_variances_all_6001_7000=readRDS(file="H2_2_gblup_variances_all_6001_7000.rds") +H2_2_gblup_variances_all_7001_8000=readRDS(file="H2_2_gblup_variances_all_7001_8000.rds") +H2_2_gblup_variances_all_8001_9000=readRDS(file="H2_2_gblup_variances_all_8001_9000.rds") +H2_2_gblup_variances_all_9001_10000=readRDS(file="H2_2_gblup_variances_all_9001_10000.rds") +H2_2_gblup_variances_all_10001_11000=readRDS(file="H2_2_gblup_variances_all_10001_11000.rds") +H2_2_gblup_variances_all_11001_12419=readRDS(file="H2_2_gblup_variances_all_11001_12419.rds") +H2_2_gblup_variances_all=c(H2_2_gblup_variances_all_1_1000,H2_2_gblup_variances_all_1001_2000,H2_2_gblup_variances_all_2001_3000,H2_2_gblup_variances_all_3001_4000,H2_2_gblup_variances_all_4001_5000,H2_2_gblup_variances_all_5001_6000,H2_2_gblup_variances_all_6001_7000,H2_2_gblup_variances_all_7001_8000,H2_2_gblup_variances_all_8001_9000,H2_2_gblup_variances_all_9001_10000,H2_2_gblup_variances_all_10001_11000,H2_2_gblup_variances_all_11001_12419) + +saveRDS(H2_2_gblup_prediction_all,"H2_2_gblup_prediction_all.rds") +saveRDS(H2_2_gblup_variances_all,"H2_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H2_2_gfblup_prediction_all_1_1000=readRDS(file="H2_2_gfblup_prediction_all_1_1000.rds") +H2_2_gfblup_prediction_all_1001_2000=readRDS(file="H2_2_gfblup_prediction_all_1001_2000.rds") +H2_2_gfblup_prediction_all_2001_3000=readRDS(file="H2_2_gfblup_prediction_all_2001_3000.rds") +H2_2_gfblup_prediction_all_3001_4000=readRDS(file="H2_2_gfblup_prediction_all_3001_4000.rds") +H2_2_gfblup_prediction_all_4001_5000=readRDS(file="H2_2_gfblup_prediction_all_4001_5000.rds") +H2_2_gfblup_prediction_all_5001_6000=readRDS(file="H2_2_gfblup_prediction_all_5001_6000.rds") +H2_2_gfblup_prediction_all_6001_7000=readRDS(file="H2_2_gfblup_prediction_all_6001_7000.rds") +H2_2_gfblup_prediction_all_7001_8000=readRDS(file="H2_2_gfblup_prediction_all_7001_8000.rds") +H2_2_gfblup_prediction_all_8001_9000=readRDS(file="H2_2_gfblup_prediction_all_8001_9000.rds") +H2_2_gfblup_prediction_all_9001_10000=readRDS(file="H2_2_gfblup_prediction_all_9001_10000.rds") +H2_2_gfblup_prediction_all_10001_11000=readRDS(file="H2_2_gfblup_prediction_all_10001_11000.rds") +H2_2_gfblup_prediction_all_11001_12419=readRDS(file="H2_2_gfblup_prediction_all_11001_12419.rds") + +H2_2_gfblup_variances_all_1_1000=readRDS(file="H2_2_gfblup_variances_all_1_1000.rds") +H2_2_gfblup_variances_all_1001_2000=readRDS(file="H2_2_gfblup_variances_all_1001_2000.rds") +H2_2_gfblup_variances_all_2001_3000=readRDS(file="H2_2_gfblup_variances_all_2001_3000.rds") +H2_2_gfblup_variances_all_3001_4000=readRDS(file="H2_2_gfblup_variances_all_3001_4000.rds") +H2_2_gfblup_variances_all_4001_5000=readRDS(file="H2_2_gfblup_variances_all_4001_5000.rds") +H2_2_gfblup_variances_all_5001_6000=readRDS(file="H2_2_gfblup_variances_all_5001_6000.rds") +H2_2_gfblup_variances_all_6001_7000=readRDS(file="H2_2_gfblup_variances_all_6001_7000.rds") +H2_2_gfblup_variances_all_7001_8000=readRDS(file="H2_2_gfblup_variances_all_7001_8000.rds") +H2_2_gfblup_variances_all_8001_9000=readRDS(file="H2_2_gfblup_variances_all_8001_9000.rds") +H2_2_gfblup_variances_all_9001_10000=readRDS(file="H2_2_gfblup_variances_all_9001_10000.rds") +H2_2_gfblup_variances_all_10001_11000=readRDS(file="H2_2_gfblup_variances_all_10001_11000.rds") +H2_2_gfblup_variances_all_11001_12419=readRDS(file="H2_2_gfblup_variances_all_11001_12419.rds") + +cycles=length(H2_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H2_2_gfblup_variances_all=rep(list(list()),cycles) +H2_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_1_1000[[r]]) + H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_1001_2000[[r]]) + H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_2001_3000[[r]]) + H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_3001_4000[[r]]) + H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_4001_5000[[r]]) + H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_5001_6000[[r]]) + H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_6001_7000[[r]]) + H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_7001_8000[[r]]) + H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_8001_9000[[r]]) + H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_9001_10000[[r]]) + H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_10001_11000[[r]]) + H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_11001_12419[[r]]) + + H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_1_1000[[r]]) + H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_1001_2000[[r]]) + H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_2001_3000[[r]]) + H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_3001_4000[[r]]) + H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_4001_5000[[r]]) + H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_5001_6000[[r]]) + H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_6001_7000[[r]]) + H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_7001_8000[[r]]) + H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_8001_9000[[r]]) + H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_9001_10000[[r]]) + H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_10001_11000[[r]]) + H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(H2_2_gfblup_prediction_all,"H2_2_gfblup_prediction_all.rds") +saveRDS(H2_2_gfblup_variances_all,"H2_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H2_3_gblup_prediction_all_1_1000=readRDS(file="H2_3_gblup_prediction_all_1_1000.rds") +H2_3_gblup_prediction_all_1001_2000=readRDS(file="H2_3_gblup_prediction_all_1001_2000.rds") +H2_3_gblup_prediction_all_2001_3000=readRDS(file="H2_3_gblup_prediction_all_2001_3000.rds") +H2_3_gblup_prediction_all_3001_4000=readRDS(file="H2_3_gblup_prediction_all_3001_4000.rds") +H2_3_gblup_prediction_all_4001_5000=readRDS(file="H2_3_gblup_prediction_all_4001_5000.rds") +H2_3_gblup_prediction_all_5001_6000=readRDS(file="H2_3_gblup_prediction_all_5001_6000.rds") +H2_3_gblup_prediction_all_6001_7000=readRDS(file="H2_3_gblup_prediction_all_6001_7000.rds") +H2_3_gblup_prediction_all_7001_8000=readRDS(file="H2_3_gblup_prediction_all_7001_8000.rds") +H2_3_gblup_prediction_all_8001_9000=readRDS(file="H2_3_gblup_prediction_all_8001_9000.rds") +H2_3_gblup_prediction_all_9001_10000=readRDS(file="H2_3_gblup_prediction_all_9001_10000.rds") +H2_3_gblup_prediction_all_10001_11000=readRDS(file="H2_3_gblup_prediction_all_10001_11000.rds") +H2_3_gblup_prediction_all_11001_12419=readRDS(file="H2_3_gblup_prediction_all_11001_12419.rds") +H2_3_gblup_prediction_all=c(H2_3_gblup_prediction_all_1_1000,H2_3_gblup_prediction_all_1001_2000,H2_3_gblup_prediction_all_2001_3000,H2_3_gblup_prediction_all_3001_4000,H2_3_gblup_prediction_all_4001_5000,H2_3_gblup_prediction_all_5001_6000,H2_3_gblup_prediction_all_6001_7000,H2_3_gblup_prediction_all_7001_8000,H2_3_gblup_prediction_all_8001_9000,H2_3_gblup_prediction_all_9001_10000,H2_3_gblup_prediction_all_10001_11000,H2_3_gblup_prediction_all_11001_12419) + +H2_3_gblup_variances_all_1_1000=readRDS(file="H2_3_gblup_variances_all_1_1000.rds") +H2_3_gblup_variances_all_1001_2000=readRDS(file="H2_3_gblup_variances_all_1001_2000.rds") +H2_3_gblup_variances_all_2001_3000=readRDS(file="H2_3_gblup_variances_all_2001_3000.rds") +H2_3_gblup_variances_all_3001_4000=readRDS(file="H2_3_gblup_variances_all_3001_4000.rds") +H2_3_gblup_variances_all_4001_5000=readRDS(file="H2_3_gblup_variances_all_4001_5000.rds") +H2_3_gblup_variances_all_5001_6000=readRDS(file="H2_3_gblup_variances_all_5001_6000.rds") +H2_3_gblup_variances_all_6001_7000=readRDS(file="H2_3_gblup_variances_all_6001_7000.rds") +H2_3_gblup_variances_all_7001_8000=readRDS(file="H2_3_gblup_variances_all_7001_8000.rds") +H2_3_gblup_variances_all_8001_9000=readRDS(file="H2_3_gblup_variances_all_8001_9000.rds") +H2_3_gblup_variances_all_9001_10000=readRDS(file="H2_3_gblup_variances_all_9001_10000.rds") +H2_3_gblup_variances_all_10001_11000=readRDS(file="H2_3_gblup_variances_all_10001_11000.rds") +H2_3_gblup_variances_all_11001_12419=readRDS(file="H2_3_gblup_variances_all_11001_12419.rds") +H2_3_gblup_variances_all=c(H2_3_gblup_variances_all_1_1000,H2_3_gblup_variances_all_1001_2000,H2_3_gblup_variances_all_2001_3000,H2_3_gblup_variances_all_3001_4000,H2_3_gblup_variances_all_4001_5000,H2_3_gblup_variances_all_5001_6000,H2_3_gblup_variances_all_6001_7000,H2_3_gblup_variances_all_7001_8000,H2_3_gblup_variances_all_8001_9000,H2_3_gblup_variances_all_9001_10000,H2_3_gblup_variances_all_10001_11000,H2_3_gblup_variances_all_11001_12419) + +saveRDS(H2_3_gblup_prediction_all,"H2_3_gblup_prediction_all.rds") +saveRDS(H2_3_gblup_variances_all,"H2_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H2_3_gfblup_prediction_all_1_1000=readRDS(file="H2_3_gfblup_prediction_all_1_1000.rds") +H2_3_gfblup_prediction_all_1001_2000=readRDS(file="H2_3_gfblup_prediction_all_1001_2000.rds") +H2_3_gfblup_prediction_all_2001_3000=readRDS(file="H2_3_gfblup_prediction_all_2001_3000.rds") +H2_3_gfblup_prediction_all_3001_4000=readRDS(file="H2_3_gfblup_prediction_all_3001_4000.rds") +H2_3_gfblup_prediction_all_4001_5000=readRDS(file="H2_3_gfblup_prediction_all_4001_5000.rds") +H2_3_gfblup_prediction_all_5001_6000=readRDS(file="H2_3_gfblup_prediction_all_5001_6000.rds") +H2_3_gfblup_prediction_all_6001_7000=readRDS(file="H2_3_gfblup_prediction_all_6001_7000.rds") +H2_3_gfblup_prediction_all_7001_8000=readRDS(file="H2_3_gfblup_prediction_all_7001_8000.rds") +H2_3_gfblup_prediction_all_8001_9000=readRDS(file="H2_3_gfblup_prediction_all_8001_9000.rds") +H2_3_gfblup_prediction_all_9001_10000=readRDS(file="H2_3_gfblup_prediction_all_9001_10000.rds") +H2_3_gfblup_prediction_all_10001_11000=readRDS(file="H2_3_gfblup_prediction_all_10001_11000.rds") +H2_3_gfblup_prediction_all_11001_12419=readRDS(file="H2_3_gfblup_prediction_all_11001_12419.rds") + +H2_3_gfblup_variances_all_1_1000=readRDS(file="H2_3_gfblup_variances_all_1_1000.rds") +H2_3_gfblup_variances_all_1001_2000=readRDS(file="H2_3_gfblup_variances_all_1001_2000.rds") +H2_3_gfblup_variances_all_2001_3000=readRDS(file="H2_3_gfblup_variances_all_2001_3000.rds") +H2_3_gfblup_variances_all_3001_4000=readRDS(file="H2_3_gfblup_variances_all_3001_4000.rds") +H2_3_gfblup_variances_all_4001_5000=readRDS(file="H2_3_gfblup_variances_all_4001_5000.rds") +H2_3_gfblup_variances_all_5001_6000=readRDS(file="H2_3_gfblup_variances_all_5001_6000.rds") +H2_3_gfblup_variances_all_6001_7000=readRDS(file="H2_3_gfblup_variances_all_6001_7000.rds") +H2_3_gfblup_variances_all_7001_8000=readRDS(file="H2_3_gfblup_variances_all_7001_8000.rds") +H2_3_gfblup_variances_all_8001_9000=readRDS(file="H2_3_gfblup_variances_all_8001_9000.rds") +H2_3_gfblup_variances_all_9001_10000=readRDS(file="H2_3_gfblup_variances_all_9001_10000.rds") +H2_3_gfblup_variances_all_10001_11000=readRDS(file="H2_3_gfblup_variances_all_10001_11000.rds") +H2_3_gfblup_variances_all_11001_12419=readRDS(file="H2_3_gfblup_variances_all_11001_12419.rds") + +cycles=length(H2_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H2_3_gfblup_variances_all=rep(list(list()),cycles) +H2_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_1_1000[[r]]) + H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_1001_2000[[r]]) + H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_2001_3000[[r]]) + H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_3001_4000[[r]]) + H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_4001_5000[[r]]) + H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_5001_6000[[r]]) + H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_6001_7000[[r]]) + H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_7001_8000[[r]]) + H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_8001_9000[[r]]) + H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_9001_10000[[r]]) + H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_10001_11000[[r]]) + H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_11001_12419[[r]]) + + H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_1_1000[[r]]) + H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_1001_2000[[r]]) + H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_2001_3000[[r]]) + H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_3001_4000[[r]]) + H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_4001_5000[[r]]) + H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_5001_6000[[r]]) + H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_6001_7000[[r]]) + H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_7001_8000[[r]]) + H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_8001_9000[[r]]) + H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_9001_10000[[r]]) + H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_10001_11000[[r]]) + H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(H2_3_gfblup_prediction_all,"H2_3_gfblup_prediction_all.rds") +saveRDS(H2_3_gfblup_variances_all,"H2_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H3_1_gblup_prediction_all_1_1000=readRDS(file="H3_1_gblup_prediction_all_1_1000.rds") +H3_1_gblup_prediction_all_1001_2000=readRDS(file="H3_1_gblup_prediction_all_1001_2000.rds") +H3_1_gblup_prediction_all_2001_3000=readRDS(file="H3_1_gblup_prediction_all_2001_3000.rds") +H3_1_gblup_prediction_all_3001_4000=readRDS(file="H3_1_gblup_prediction_all_3001_4000.rds") +H3_1_gblup_prediction_all_4001_5000=readRDS(file="H3_1_gblup_prediction_all_4001_5000.rds") +H3_1_gblup_prediction_all_5001_6000=readRDS(file="H3_1_gblup_prediction_all_5001_6000.rds") +H3_1_gblup_prediction_all_6001_7000=readRDS(file="H3_1_gblup_prediction_all_6001_7000.rds") +H3_1_gblup_prediction_all_7001_8000=readRDS(file="H3_1_gblup_prediction_all_7001_8000.rds") +H3_1_gblup_prediction_all_8001_9000=readRDS(file="H3_1_gblup_prediction_all_8001_9000.rds") +H3_1_gblup_prediction_all_9001_10000=readRDS(file="H3_1_gblup_prediction_all_9001_10000.rds") +H3_1_gblup_prediction_all_10001_11000=readRDS(file="H3_1_gblup_prediction_all_10001_11000.rds") +H3_1_gblup_prediction_all_11001_12419=readRDS(file="H3_1_gblup_prediction_all_11001_12419.rds") +H3_1_gblup_prediction_all=c(H3_1_gblup_prediction_all_1_1000,H3_1_gblup_prediction_all_1001_2000,H3_1_gblup_prediction_all_2001_3000,H3_1_gblup_prediction_all_3001_4000,H3_1_gblup_prediction_all_4001_5000,H3_1_gblup_prediction_all_5001_6000,H3_1_gblup_prediction_all_6001_7000,H3_1_gblup_prediction_all_7001_8000,H3_1_gblup_prediction_all_8001_9000,H3_1_gblup_prediction_all_9001_10000,H3_1_gblup_prediction_all_10001_11000,H3_1_gblup_prediction_all_11001_12419) + +H3_1_gblup_variances_all_1_1000=readRDS(file="H3_1_gblup_variances_all_1_1000.rds") +H3_1_gblup_variances_all_1001_2000=readRDS(file="H3_1_gblup_variances_all_1001_2000.rds") +H3_1_gblup_variances_all_2001_3000=readRDS(file="H3_1_gblup_variances_all_2001_3000.rds") +H3_1_gblup_variances_all_3001_4000=readRDS(file="H3_1_gblup_variances_all_3001_4000.rds") +H3_1_gblup_variances_all_4001_5000=readRDS(file="H3_1_gblup_variances_all_4001_5000.rds") +H3_1_gblup_variances_all_5001_6000=readRDS(file="H3_1_gblup_variances_all_5001_6000.rds") +H3_1_gblup_variances_all_6001_7000=readRDS(file="H3_1_gblup_variances_all_6001_7000.rds") +H3_1_gblup_variances_all_7001_8000=readRDS(file="H3_1_gblup_variances_all_7001_8000.rds") +H3_1_gblup_variances_all_8001_9000=readRDS(file="H3_1_gblup_variances_all_8001_9000.rds") +H3_1_gblup_variances_all_9001_10000=readRDS(file="H3_1_gblup_variances_all_9001_10000.rds") +H3_1_gblup_variances_all_10001_11000=readRDS(file="H3_1_gblup_variances_all_10001_11000.rds") +H3_1_gblup_variances_all_11001_12419=readRDS(file="H3_1_gblup_variances_all_11001_12419.rds") +H3_1_gblup_variances_all=c(H3_1_gblup_variances_all_1_1000,H3_1_gblup_variances_all_1001_2000,H3_1_gblup_variances_all_2001_3000,H3_1_gblup_variances_all_3001_4000,H3_1_gblup_variances_all_4001_5000,H3_1_gblup_variances_all_5001_6000,H3_1_gblup_variances_all_6001_7000,H3_1_gblup_variances_all_7001_8000,H3_1_gblup_variances_all_8001_9000,H3_1_gblup_variances_all_9001_10000,H3_1_gblup_variances_all_10001_11000,H3_1_gblup_variances_all_11001_12419) + +saveRDS(H3_1_gblup_prediction_all,"H3_1_gblup_prediction_all.rds") +saveRDS(H3_1_gblup_variances_all,"H3_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H3_1_gfblup_prediction_all_1_1000=readRDS(file="H3_1_gfblup_prediction_all_1_1000.rds") +H3_1_gfblup_prediction_all_1001_2000=readRDS(file="H3_1_gfblup_prediction_all_1001_2000.rds") +H3_1_gfblup_prediction_all_2001_3000=readRDS(file="H3_1_gfblup_prediction_all_2001_3000.rds") +H3_1_gfblup_prediction_all_3001_4000=readRDS(file="H3_1_gfblup_prediction_all_3001_4000.rds") +H3_1_gfblup_prediction_all_4001_5000=readRDS(file="H3_1_gfblup_prediction_all_4001_5000.rds") +H3_1_gfblup_prediction_all_5001_6000=readRDS(file="H3_1_gfblup_prediction_all_5001_6000.rds") +H3_1_gfblup_prediction_all_6001_7000=readRDS(file="H3_1_gfblup_prediction_all_6001_7000.rds") +H3_1_gfblup_prediction_all_7001_8000=readRDS(file="H3_1_gfblup_prediction_all_7001_8000.rds") +H3_1_gfblup_prediction_all_8001_9000=readRDS(file="H3_1_gfblup_prediction_all_8001_9000.rds") +H3_1_gfblup_prediction_all_9001_10000=readRDS(file="H3_1_gfblup_prediction_all_9001_10000.rds") +H3_1_gfblup_prediction_all_10001_11000=readRDS(file="H3_1_gfblup_prediction_all_10001_11000.rds") +H3_1_gfblup_prediction_all_11001_12419=readRDS(file="H3_1_gfblup_prediction_all_11001_12419.rds") + +H3_1_gfblup_variances_all_1_1000=readRDS(file="H3_1_gfblup_variances_all_1_1000.rds") +H3_1_gfblup_variances_all_1001_2000=readRDS(file="H3_1_gfblup_variances_all_1001_2000.rds") +H3_1_gfblup_variances_all_2001_3000=readRDS(file="H3_1_gfblup_variances_all_2001_3000.rds") +H3_1_gfblup_variances_all_3001_4000=readRDS(file="H3_1_gfblup_variances_all_3001_4000.rds") +H3_1_gfblup_variances_all_4001_5000=readRDS(file="H3_1_gfblup_variances_all_4001_5000.rds") +H3_1_gfblup_variances_all_5001_6000=readRDS(file="H3_1_gfblup_variances_all_5001_6000.rds") +H3_1_gfblup_variances_all_6001_7000=readRDS(file="H3_1_gfblup_variances_all_6001_7000.rds") +H3_1_gfblup_variances_all_7001_8000=readRDS(file="H3_1_gfblup_variances_all_7001_8000.rds") +H3_1_gfblup_variances_all_8001_9000=readRDS(file="H3_1_gfblup_variances_all_8001_9000.rds") +H3_1_gfblup_variances_all_9001_10000=readRDS(file="H3_1_gfblup_variances_all_9001_10000.rds") +H3_1_gfblup_variances_all_10001_11000=readRDS(file="H3_1_gfblup_variances_all_10001_11000.rds") +H3_1_gfblup_variances_all_11001_12419=readRDS(file="H3_1_gfblup_variances_all_11001_12419.rds") + +cycles=length(H3_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H3_1_gfblup_variances_all=rep(list(list()),cycles) +H3_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_1_1000[[r]]) + H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_1001_2000[[r]]) + H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_2001_3000[[r]]) + H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_3001_4000[[r]]) + H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_4001_5000[[r]]) + H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_5001_6000[[r]]) + H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_6001_7000[[r]]) + H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_7001_8000[[r]]) + H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_8001_9000[[r]]) + H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_9001_10000[[r]]) + H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_10001_11000[[r]]) + H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_11001_12419[[r]]) + + H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_1_1000[[r]]) + H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_1001_2000[[r]]) + H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_2001_3000[[r]]) + H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_3001_4000[[r]]) + H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_4001_5000[[r]]) + H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_5001_6000[[r]]) + H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_6001_7000[[r]]) + H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_7001_8000[[r]]) + H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_8001_9000[[r]]) + H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_9001_10000[[r]]) + H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_10001_11000[[r]]) + H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(H3_1_gfblup_prediction_all,"H3_1_gfblup_prediction_all.rds") +saveRDS(H3_1_gfblup_variances_all,"H3_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H3_2_gblup_prediction_all_1_1000=readRDS(file="H3_2_gblup_prediction_all_1_1000.rds") +H3_2_gblup_prediction_all_1001_2000=readRDS(file="H3_2_gblup_prediction_all_1001_2000.rds") +H3_2_gblup_prediction_all_2001_3000=readRDS(file="H3_2_gblup_prediction_all_2001_3000.rds") +H3_2_gblup_prediction_all_3001_4000=readRDS(file="H3_2_gblup_prediction_all_3001_4000.rds") +H3_2_gblup_prediction_all_4001_5000=readRDS(file="H3_2_gblup_prediction_all_4001_5000.rds") +H3_2_gblup_prediction_all_5001_6000=readRDS(file="H3_2_gblup_prediction_all_5001_6000.rds") +H3_2_gblup_prediction_all_6001_7000=readRDS(file="H3_2_gblup_prediction_all_6001_7000.rds") +H3_2_gblup_prediction_all_7001_8000=readRDS(file="H3_2_gblup_prediction_all_7001_8000.rds") +H3_2_gblup_prediction_all_8001_9000=readRDS(file="H3_2_gblup_prediction_all_8001_9000.rds") +H3_2_gblup_prediction_all_9001_10000=readRDS(file="H3_2_gblup_prediction_all_9001_10000.rds") +H3_2_gblup_prediction_all_10001_11000=readRDS(file="H3_2_gblup_prediction_all_10001_11000.rds") +H3_2_gblup_prediction_all_11001_12419=readRDS(file="H3_2_gblup_prediction_all_11001_12419.rds") +H3_2_gblup_prediction_all=c(H3_2_gblup_prediction_all_1_1000,H3_2_gblup_prediction_all_1001_2000,H3_2_gblup_prediction_all_2001_3000,H3_2_gblup_prediction_all_3001_4000,H3_2_gblup_prediction_all_4001_5000,H3_2_gblup_prediction_all_5001_6000,H3_2_gblup_prediction_all_6001_7000,H3_2_gblup_prediction_all_7001_8000,H3_2_gblup_prediction_all_8001_9000,H3_2_gblup_prediction_all_9001_10000,H3_2_gblup_prediction_all_10001_11000,H3_2_gblup_prediction_all_11001_12419) + +H3_2_gblup_variances_all_1_1000=readRDS(file="H3_2_gblup_variances_all_1_1000.rds") +H3_2_gblup_variances_all_1001_2000=readRDS(file="H3_2_gblup_variances_all_1001_2000.rds") +H3_2_gblup_variances_all_2001_3000=readRDS(file="H3_2_gblup_variances_all_2001_3000.rds") +H3_2_gblup_variances_all_3001_4000=readRDS(file="H3_2_gblup_variances_all_3001_4000.rds") +H3_2_gblup_variances_all_4001_5000=readRDS(file="H3_2_gblup_variances_all_4001_5000.rds") +H3_2_gblup_variances_all_5001_6000=readRDS(file="H3_2_gblup_variances_all_5001_6000.rds") +H3_2_gblup_variances_all_6001_7000=readRDS(file="H3_2_gblup_variances_all_6001_7000.rds") +H3_2_gblup_variances_all_7001_8000=readRDS(file="H3_2_gblup_variances_all_7001_8000.rds") +H3_2_gblup_variances_all_8001_9000=readRDS(file="H3_2_gblup_variances_all_8001_9000.rds") +H3_2_gblup_variances_all_9001_10000=readRDS(file="H3_2_gblup_variances_all_9001_10000.rds") +H3_2_gblup_variances_all_10001_11000=readRDS(file="H3_2_gblup_variances_all_10001_11000.rds") +H3_2_gblup_variances_all_11001_12419=readRDS(file="H3_2_gblup_variances_all_11001_12419.rds") +H3_2_gblup_variances_all=c(H3_2_gblup_variances_all_1_1000,H3_2_gblup_variances_all_1001_2000,H3_2_gblup_variances_all_2001_3000,H3_2_gblup_variances_all_3001_4000,H3_2_gblup_variances_all_4001_5000,H3_2_gblup_variances_all_5001_6000,H3_2_gblup_variances_all_6001_7000,H3_2_gblup_variances_all_7001_8000,H3_2_gblup_variances_all_8001_9000,H3_2_gblup_variances_all_9001_10000,H3_2_gblup_variances_all_10001_11000,H3_2_gblup_variances_all_11001_12419) + +saveRDS(H3_2_gblup_prediction_all,"H3_2_gblup_prediction_all.rds") +saveRDS(H3_2_gblup_variances_all,"H3_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H3_2_gfblup_prediction_all_1_1000=readRDS(file="H3_2_gfblup_prediction_all_1_1000.rds") +H3_2_gfblup_prediction_all_1001_2000=readRDS(file="H3_2_gfblup_prediction_all_1001_2000.rds") +H3_2_gfblup_prediction_all_2001_3000=readRDS(file="H3_2_gfblup_prediction_all_2001_3000.rds") +H3_2_gfblup_prediction_all_3001_4000=readRDS(file="H3_2_gfblup_prediction_all_3001_4000.rds") +H3_2_gfblup_prediction_all_4001_5000=readRDS(file="H3_2_gfblup_prediction_all_4001_5000.rds") +H3_2_gfblup_prediction_all_5001_6000=readRDS(file="H3_2_gfblup_prediction_all_5001_6000.rds") +H3_2_gfblup_prediction_all_6001_7000=readRDS(file="H3_2_gfblup_prediction_all_6001_7000.rds") +H3_2_gfblup_prediction_all_7001_8000=readRDS(file="H3_2_gfblup_prediction_all_7001_8000.rds") +H3_2_gfblup_prediction_all_8001_9000=readRDS(file="H3_2_gfblup_prediction_all_8001_9000.rds") +H3_2_gfblup_prediction_all_9001_10000=readRDS(file="H3_2_gfblup_prediction_all_9001_10000.rds") +H3_2_gfblup_prediction_all_10001_11000=readRDS(file="H3_2_gfblup_prediction_all_10001_11000.rds") +H3_2_gfblup_prediction_all_11001_12419=readRDS(file="H3_2_gfblup_prediction_all_11001_12419.rds") + +H3_2_gfblup_variances_all_1_1000=readRDS(file="H3_2_gfblup_variances_all_1_1000.rds") +H3_2_gfblup_variances_all_1001_2000=readRDS(file="H3_2_gfblup_variances_all_1001_2000.rds") +H3_2_gfblup_variances_all_2001_3000=readRDS(file="H3_2_gfblup_variances_all_2001_3000.rds") +H3_2_gfblup_variances_all_3001_4000=readRDS(file="H3_2_gfblup_variances_all_3001_4000.rds") +H3_2_gfblup_variances_all_4001_5000=readRDS(file="H3_2_gfblup_variances_all_4001_5000.rds") +H3_2_gfblup_variances_all_5001_6000=readRDS(file="H3_2_gfblup_variances_all_5001_6000.rds") +H3_2_gfblup_variances_all_6001_7000=readRDS(file="H3_2_gfblup_variances_all_6001_7000.rds") +H3_2_gfblup_variances_all_7001_8000=readRDS(file="H3_2_gfblup_variances_all_7001_8000.rds") +H3_2_gfblup_variances_all_8001_9000=readRDS(file="H3_2_gfblup_variances_all_8001_9000.rds") +H3_2_gfblup_variances_all_9001_10000=readRDS(file="H3_2_gfblup_variances_all_9001_10000.rds") +H3_2_gfblup_variances_all_10001_11000=readRDS(file="H3_2_gfblup_variances_all_10001_11000.rds") +H3_2_gfblup_variances_all_11001_12419=readRDS(file="H3_2_gfblup_variances_all_11001_12419.rds") + +cycles=length(H3_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H3_2_gfblup_variances_all=rep(list(list()),cycles) +H3_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_1_1000[[r]]) + H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_1001_2000[[r]]) + H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_2001_3000[[r]]) + H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_3001_4000[[r]]) + H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_4001_5000[[r]]) + H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_5001_6000[[r]]) + H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_6001_7000[[r]]) + H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_7001_8000[[r]]) + H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_8001_9000[[r]]) + H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_9001_10000[[r]]) + H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_10001_11000[[r]]) + H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_11001_12419[[r]]) + + H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_1_1000[[r]]) + H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_1001_2000[[r]]) + H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_2001_3000[[r]]) + H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_3001_4000[[r]]) + H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_4001_5000[[r]]) + H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_5001_6000[[r]]) + H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_6001_7000[[r]]) + H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_7001_8000[[r]]) + H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_8001_9000[[r]]) + H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_9001_10000[[r]]) + H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_10001_11000[[r]]) + H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(H3_2_gfblup_prediction_all,"H3_2_gfblup_prediction_all.rds") +saveRDS(H3_2_gfblup_variances_all,"H3_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H3_3_gblup_prediction_all_1_1000=readRDS(file="H3_3_gblup_prediction_all_1_1000.rds") +H3_3_gblup_prediction_all_1001_2000=readRDS(file="H3_3_gblup_prediction_all_1001_2000.rds") +H3_3_gblup_prediction_all_2001_3000=readRDS(file="H3_3_gblup_prediction_all_2001_3000.rds") +H3_3_gblup_prediction_all_3001_4000=readRDS(file="H3_3_gblup_prediction_all_3001_4000.rds") +H3_3_gblup_prediction_all_4001_5000=readRDS(file="H3_3_gblup_prediction_all_4001_5000.rds") +H3_3_gblup_prediction_all_5001_6000=readRDS(file="H3_3_gblup_prediction_all_5001_6000.rds") +H3_3_gblup_prediction_all_6001_7000=readRDS(file="H3_3_gblup_prediction_all_6001_7000.rds") +H3_3_gblup_prediction_all_7001_8000=readRDS(file="H3_3_gblup_prediction_all_7001_8000.rds") +H3_3_gblup_prediction_all_8001_9000=readRDS(file="H3_3_gblup_prediction_all_8001_9000.rds") +H3_3_gblup_prediction_all_9001_10000=readRDS(file="H3_3_gblup_prediction_all_9001_10000.rds") +H3_3_gblup_prediction_all_10001_11000=readRDS(file="H3_3_gblup_prediction_all_10001_11000.rds") +H3_3_gblup_prediction_all_11001_12419=readRDS(file="H3_3_gblup_prediction_all_11001_12419.rds") +H3_3_gblup_prediction_all=c(H3_3_gblup_prediction_all_1_1000,H3_3_gblup_prediction_all_1001_2000,H3_3_gblup_prediction_all_2001_3000,H3_3_gblup_prediction_all_3001_4000,H3_3_gblup_prediction_all_4001_5000,H3_3_gblup_prediction_all_5001_6000,H3_3_gblup_prediction_all_6001_7000,H3_3_gblup_prediction_all_7001_8000,H3_3_gblup_prediction_all_8001_9000,H3_3_gblup_prediction_all_9001_10000,H3_3_gblup_prediction_all_10001_11000,H3_3_gblup_prediction_all_11001_12419) + +H3_3_gblup_variances_all_1_1000=readRDS(file="H3_3_gblup_variances_all_1_1000.rds") +H3_3_gblup_variances_all_1001_2000=readRDS(file="H3_3_gblup_variances_all_1001_2000.rds") +H3_3_gblup_variances_all_2001_3000=readRDS(file="H3_3_gblup_variances_all_2001_3000.rds") +H3_3_gblup_variances_all_3001_4000=readRDS(file="H3_3_gblup_variances_all_3001_4000.rds") +H3_3_gblup_variances_all_4001_5000=readRDS(file="H3_3_gblup_variances_all_4001_5000.rds") +H3_3_gblup_variances_all_5001_6000=readRDS(file="H3_3_gblup_variances_all_5001_6000.rds") +H3_3_gblup_variances_all_6001_7000=readRDS(file="H3_3_gblup_variances_all_6001_7000.rds") +H3_3_gblup_variances_all_7001_8000=readRDS(file="H3_3_gblup_variances_all_7001_8000.rds") +H3_3_gblup_variances_all_8001_9000=readRDS(file="H3_3_gblup_variances_all_8001_9000.rds") +H3_3_gblup_variances_all_9001_10000=readRDS(file="H3_3_gblup_variances_all_9001_10000.rds") +H3_3_gblup_variances_all_10001_11000=readRDS(file="H3_3_gblup_variances_all_10001_11000.rds") +H3_3_gblup_variances_all_11001_12419=readRDS(file="H3_3_gblup_variances_all_11001_12419.rds") +H3_3_gblup_variances_all=c(H3_3_gblup_variances_all_1_1000,H3_3_gblup_variances_all_1001_2000,H3_3_gblup_variances_all_2001_3000,H3_3_gblup_variances_all_3001_4000,H3_3_gblup_variances_all_4001_5000,H3_3_gblup_variances_all_5001_6000,H3_3_gblup_variances_all_6001_7000,H3_3_gblup_variances_all_7001_8000,H3_3_gblup_variances_all_8001_9000,H3_3_gblup_variances_all_9001_10000,H3_3_gblup_variances_all_10001_11000,H3_3_gblup_variances_all_11001_12419) + +saveRDS(H3_3_gblup_prediction_all,"H3_3_gblup_prediction_all.rds") +saveRDS(H3_3_gblup_variances_all,"H3_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H3_3_gfblup_prediction_all_1_1000=readRDS(file="H3_3_gfblup_prediction_all_1_1000.rds") +H3_3_gfblup_prediction_all_1001_2000=readRDS(file="H3_3_gfblup_prediction_all_1001_2000.rds") +H3_3_gfblup_prediction_all_2001_3000=readRDS(file="H3_3_gfblup_prediction_all_2001_3000.rds") +H3_3_gfblup_prediction_all_3001_4000=readRDS(file="H3_3_gfblup_prediction_all_3001_4000.rds") +H3_3_gfblup_prediction_all_4001_5000=readRDS(file="H3_3_gfblup_prediction_all_4001_5000.rds") +H3_3_gfblup_prediction_all_5001_6000=readRDS(file="H3_3_gfblup_prediction_all_5001_6000.rds") +H3_3_gfblup_prediction_all_6001_7000=readRDS(file="H3_3_gfblup_prediction_all_6001_7000.rds") +H3_3_gfblup_prediction_all_7001_8000=readRDS(file="H3_3_gfblup_prediction_all_7001_8000.rds") +H3_3_gfblup_prediction_all_8001_9000=readRDS(file="H3_3_gfblup_prediction_all_8001_9000.rds") +H3_3_gfblup_prediction_all_9001_10000=readRDS(file="H3_3_gfblup_prediction_all_9001_10000.rds") +H3_3_gfblup_prediction_all_10001_11000=readRDS(file="H3_3_gfblup_prediction_all_10001_11000.rds") +H3_3_gfblup_prediction_all_11001_12419=readRDS(file="H3_3_gfblup_prediction_all_11001_12419.rds") + +H3_3_gfblup_variances_all_1_1000=readRDS(file="H3_3_gfblup_variances_all_1_1000.rds") +H3_3_gfblup_variances_all_1001_2000=readRDS(file="H3_3_gfblup_variances_all_1001_2000.rds") +H3_3_gfblup_variances_all_2001_3000=readRDS(file="H3_3_gfblup_variances_all_2001_3000.rds") +H3_3_gfblup_variances_all_3001_4000=readRDS(file="H3_3_gfblup_variances_all_3001_4000.rds") +H3_3_gfblup_variances_all_4001_5000=readRDS(file="H3_3_gfblup_variances_all_4001_5000.rds") +H3_3_gfblup_variances_all_5001_6000=readRDS(file="H3_3_gfblup_variances_all_5001_6000.rds") +H3_3_gfblup_variances_all_6001_7000=readRDS(file="H3_3_gfblup_variances_all_6001_7000.rds") +H3_3_gfblup_variances_all_7001_8000=readRDS(file="H3_3_gfblup_variances_all_7001_8000.rds") +H3_3_gfblup_variances_all_8001_9000=readRDS(file="H3_3_gfblup_variances_all_8001_9000.rds") +H3_3_gfblup_variances_all_9001_10000=readRDS(file="H3_3_gfblup_variances_all_9001_10000.rds") +H3_3_gfblup_variances_all_10001_11000=readRDS(file="H3_3_gfblup_variances_all_10001_11000.rds") +H3_3_gfblup_variances_all_11001_12419=readRDS(file="H3_3_gfblup_variances_all_11001_12419.rds") + +cycles=length(H3_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H3_3_gfblup_variances_all=rep(list(list()),cycles) +H3_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_1_1000[[r]]) + H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_1001_2000[[r]]) + H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_2001_3000[[r]]) + H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_3001_4000[[r]]) + H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_4001_5000[[r]]) + H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_5001_6000[[r]]) + H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_6001_7000[[r]]) + H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_7001_8000[[r]]) + H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_8001_9000[[r]]) + H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_9001_10000[[r]]) + H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_10001_11000[[r]]) + H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_11001_12419[[r]]) + + H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_1_1000[[r]]) + H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_1001_2000[[r]]) + H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_2001_3000[[r]]) + H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_3001_4000[[r]]) + H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_4001_5000[[r]]) + H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_5001_6000[[r]]) + H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_6001_7000[[r]]) + H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_7001_8000[[r]]) + H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_8001_9000[[r]]) + H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_9001_10000[[r]]) + H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_10001_11000[[r]]) + H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(H3_3_gfblup_prediction_all,"H3_3_gfblup_prediction_all.rds") +saveRDS(H3_3_gfblup_variances_all,"H3_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H4_1_gblup_prediction_all_1_1000=readRDS(file="H4_1_gblup_prediction_all_1_1000.rds") +H4_1_gblup_prediction_all_1001_2000=readRDS(file="H4_1_gblup_prediction_all_1001_2000.rds") +H4_1_gblup_prediction_all_2001_3000=readRDS(file="H4_1_gblup_prediction_all_2001_3000.rds") +H4_1_gblup_prediction_all_3001_4000=readRDS(file="H4_1_gblup_prediction_all_3001_4000.rds") +H4_1_gblup_prediction_all_4001_5000=readRDS(file="H4_1_gblup_prediction_all_4001_5000.rds") +H4_1_gblup_prediction_all_5001_6000=readRDS(file="H4_1_gblup_prediction_all_5001_6000.rds") +H4_1_gblup_prediction_all_6001_7000=readRDS(file="H4_1_gblup_prediction_all_6001_7000.rds") +H4_1_gblup_prediction_all_7001_8000=readRDS(file="H4_1_gblup_prediction_all_7001_8000.rds") +H4_1_gblup_prediction_all_8001_9000=readRDS(file="H4_1_gblup_prediction_all_8001_9000.rds") +H4_1_gblup_prediction_all_9001_10000=readRDS(file="H4_1_gblup_prediction_all_9001_10000.rds") +H4_1_gblup_prediction_all_10001_11000=readRDS(file="H4_1_gblup_prediction_all_10001_11000.rds") +H4_1_gblup_prediction_all_11001_12419=readRDS(file="H4_1_gblup_prediction_all_11001_12419.rds") +H4_1_gblup_prediction_all=c(H4_1_gblup_prediction_all_1_1000,H4_1_gblup_prediction_all_1001_2000,H4_1_gblup_prediction_all_2001_3000,H4_1_gblup_prediction_all_3001_4000,H4_1_gblup_prediction_all_4001_5000,H4_1_gblup_prediction_all_5001_6000,H4_1_gblup_prediction_all_6001_7000,H4_1_gblup_prediction_all_7001_8000,H4_1_gblup_prediction_all_8001_9000,H4_1_gblup_prediction_all_9001_10000,H4_1_gblup_prediction_all_10001_11000,H4_1_gblup_prediction_all_11001_12419) + +H4_1_gblup_variances_all_1_1000=readRDS(file="H4_1_gblup_variances_all_1_1000.rds") +H4_1_gblup_variances_all_1001_2000=readRDS(file="H4_1_gblup_variances_all_1001_2000.rds") +H4_1_gblup_variances_all_2001_3000=readRDS(file="H4_1_gblup_variances_all_2001_3000.rds") +H4_1_gblup_variances_all_3001_4000=readRDS(file="H4_1_gblup_variances_all_3001_4000.rds") +H4_1_gblup_variances_all_4001_5000=readRDS(file="H4_1_gblup_variances_all_4001_5000.rds") +H4_1_gblup_variances_all_5001_6000=readRDS(file="H4_1_gblup_variances_all_5001_6000.rds") +H4_1_gblup_variances_all_6001_7000=readRDS(file="H4_1_gblup_variances_all_6001_7000.rds") +H4_1_gblup_variances_all_7001_8000=readRDS(file="H4_1_gblup_variances_all_7001_8000.rds") +H4_1_gblup_variances_all_8001_9000=readRDS(file="H4_1_gblup_variances_all_8001_9000.rds") +H4_1_gblup_variances_all_9001_10000=readRDS(file="H4_1_gblup_variances_all_9001_10000.rds") +H4_1_gblup_variances_all_10001_11000=readRDS(file="H4_1_gblup_variances_all_10001_11000.rds") +H4_1_gblup_variances_all_11001_12419=readRDS(file="H4_1_gblup_variances_all_11001_12419.rds") +H4_1_gblup_variances_all=c(H4_1_gblup_variances_all_1_1000,H4_1_gblup_variances_all_1001_2000,H4_1_gblup_variances_all_2001_3000,H4_1_gblup_variances_all_3001_4000,H4_1_gblup_variances_all_4001_5000,H4_1_gblup_variances_all_5001_6000,H4_1_gblup_variances_all_6001_7000,H4_1_gblup_variances_all_7001_8000,H4_1_gblup_variances_all_8001_9000,H4_1_gblup_variances_all_9001_10000,H4_1_gblup_variances_all_10001_11000,H4_1_gblup_variances_all_11001_12419) + +saveRDS(H4_1_gblup_prediction_all,"H4_1_gblup_prediction_all.rds") +saveRDS(H4_1_gblup_variances_all,"H4_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H4_1_gfblup_prediction_all_1_1000=readRDS(file="H4_1_gfblup_prediction_all_1_1000.rds") +H4_1_gfblup_prediction_all_1001_2000=readRDS(file="H4_1_gfblup_prediction_all_1001_2000.rds") +H4_1_gfblup_prediction_all_2001_3000=readRDS(file="H4_1_gfblup_prediction_all_2001_3000.rds") +H4_1_gfblup_prediction_all_3001_4000=readRDS(file="H4_1_gfblup_prediction_all_3001_4000.rds") +H4_1_gfblup_prediction_all_4001_5000=readRDS(file="H4_1_gfblup_prediction_all_4001_5000.rds") +H4_1_gfblup_prediction_all_5001_6000=readRDS(file="H4_1_gfblup_prediction_all_5001_6000.rds") +H4_1_gfblup_prediction_all_6001_7000=readRDS(file="H4_1_gfblup_prediction_all_6001_7000.rds") +H4_1_gfblup_prediction_all_7001_8000=readRDS(file="H4_1_gfblup_prediction_all_7001_8000.rds") +H4_1_gfblup_prediction_all_8001_9000=readRDS(file="H4_1_gfblup_prediction_all_8001_9000.rds") +H4_1_gfblup_prediction_all_9001_10000=readRDS(file="H4_1_gfblup_prediction_all_9001_10000.rds") +H4_1_gfblup_prediction_all_10001_11000=readRDS(file="H4_1_gfblup_prediction_all_10001_11000.rds") +H4_1_gfblup_prediction_all_11001_12419=readRDS(file="H4_1_gfblup_prediction_all_11001_12419.rds") + +H4_1_gfblup_variances_all_1_1000=readRDS(file="H4_1_gfblup_variances_all_1_1000.rds") +H4_1_gfblup_variances_all_1001_2000=readRDS(file="H4_1_gfblup_variances_all_1001_2000.rds") +H4_1_gfblup_variances_all_2001_3000=readRDS(file="H4_1_gfblup_variances_all_2001_3000.rds") +H4_1_gfblup_variances_all_3001_4000=readRDS(file="H4_1_gfblup_variances_all_3001_4000.rds") +H4_1_gfblup_variances_all_4001_5000=readRDS(file="H4_1_gfblup_variances_all_4001_5000.rds") +H4_1_gfblup_variances_all_5001_6000=readRDS(file="H4_1_gfblup_variances_all_5001_6000.rds") +H4_1_gfblup_variances_all_6001_7000=readRDS(file="H4_1_gfblup_variances_all_6001_7000.rds") +H4_1_gfblup_variances_all_7001_8000=readRDS(file="H4_1_gfblup_variances_all_7001_8000.rds") +H4_1_gfblup_variances_all_8001_9000=readRDS(file="H4_1_gfblup_variances_all_8001_9000.rds") +H4_1_gfblup_variances_all_9001_10000=readRDS(file="H4_1_gfblup_variances_all_9001_10000.rds") +H4_1_gfblup_variances_all_10001_11000=readRDS(file="H4_1_gfblup_variances_all_10001_11000.rds") +H4_1_gfblup_variances_all_11001_12419=readRDS(file="H4_1_gfblup_variances_all_11001_12419.rds") + +cycles=length(H4_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H4_1_gfblup_variances_all=rep(list(list()),cycles) +H4_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_1_1000[[r]]) + H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_1001_2000[[r]]) + H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_2001_3000[[r]]) + H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_3001_4000[[r]]) + H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_4001_5000[[r]]) + H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_5001_6000[[r]]) + H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_6001_7000[[r]]) + H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_7001_8000[[r]]) + H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_8001_9000[[r]]) + H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_9001_10000[[r]]) + H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_10001_11000[[r]]) + H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_11001_12419[[r]]) + + H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_1_1000[[r]]) + H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_1001_2000[[r]]) + H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_2001_3000[[r]]) + H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_3001_4000[[r]]) + H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_4001_5000[[r]]) + H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_5001_6000[[r]]) + H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_6001_7000[[r]]) + H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_7001_8000[[r]]) + H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_8001_9000[[r]]) + H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_9001_10000[[r]]) + H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_10001_11000[[r]]) + H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(H4_1_gfblup_prediction_all,"H4_1_gfblup_prediction_all.rds") +saveRDS(H4_1_gfblup_variances_all,"H4_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H4_2_gblup_prediction_all_1_1000=readRDS(file="H4_2_gblup_prediction_all_1_1000.rds") +H4_2_gblup_prediction_all_1001_2000=readRDS(file="H4_2_gblup_prediction_all_1001_2000.rds") +H4_2_gblup_prediction_all_2001_3000=readRDS(file="H4_2_gblup_prediction_all_2001_3000.rds") +H4_2_gblup_prediction_all_3001_4000=readRDS(file="H4_2_gblup_prediction_all_3001_4000.rds") +H4_2_gblup_prediction_all_4001_5000=readRDS(file="H4_2_gblup_prediction_all_4001_5000.rds") +H4_2_gblup_prediction_all_5001_6000=readRDS(file="H4_2_gblup_prediction_all_5001_6000.rds") +H4_2_gblup_prediction_all_6001_7000=readRDS(file="H4_2_gblup_prediction_all_6001_7000.rds") +H4_2_gblup_prediction_all_7001_8000=readRDS(file="H4_2_gblup_prediction_all_7001_8000.rds") +H4_2_gblup_prediction_all_8001_9000=readRDS(file="H4_2_gblup_prediction_all_8001_9000.rds") +H4_2_gblup_prediction_all_9001_10000=readRDS(file="H4_2_gblup_prediction_all_9001_10000.rds") +H4_2_gblup_prediction_all_10001_11000=readRDS(file="H4_2_gblup_prediction_all_10001_11000.rds") +H4_2_gblup_prediction_all_11001_12419=readRDS(file="H4_2_gblup_prediction_all_11001_12419.rds") +H4_2_gblup_prediction_all=c(H4_2_gblup_prediction_all_1_1000,H4_2_gblup_prediction_all_1001_2000,H4_2_gblup_prediction_all_2001_3000,H4_2_gblup_prediction_all_3001_4000,H4_2_gblup_prediction_all_4001_5000,H4_2_gblup_prediction_all_5001_6000,H4_2_gblup_prediction_all_6001_7000,H4_2_gblup_prediction_all_7001_8000,H4_2_gblup_prediction_all_8001_9000,H4_2_gblup_prediction_all_9001_10000,H4_2_gblup_prediction_all_10001_11000,H4_2_gblup_prediction_all_11001_12419) + +H4_2_gblup_variances_all_1_1000=readRDS(file="H4_2_gblup_variances_all_1_1000.rds") +H4_2_gblup_variances_all_1001_2000=readRDS(file="H4_2_gblup_variances_all_1001_2000.rds") +H4_2_gblup_variances_all_2001_3000=readRDS(file="H4_2_gblup_variances_all_2001_3000.rds") +H4_2_gblup_variances_all_3001_4000=readRDS(file="H4_2_gblup_variances_all_3001_4000.rds") +H4_2_gblup_variances_all_4001_5000=readRDS(file="H4_2_gblup_variances_all_4001_5000.rds") +H4_2_gblup_variances_all_5001_6000=readRDS(file="H4_2_gblup_variances_all_5001_6000.rds") +H4_2_gblup_variances_all_6001_7000=readRDS(file="H4_2_gblup_variances_all_6001_7000.rds") +H4_2_gblup_variances_all_7001_8000=readRDS(file="H4_2_gblup_variances_all_7001_8000.rds") +H4_2_gblup_variances_all_8001_9000=readRDS(file="H4_2_gblup_variances_all_8001_9000.rds") +H4_2_gblup_variances_all_9001_10000=readRDS(file="H4_2_gblup_variances_all_9001_10000.rds") +H4_2_gblup_variances_all_10001_11000=readRDS(file="H4_2_gblup_variances_all_10001_11000.rds") +H4_2_gblup_variances_all_11001_12419=readRDS(file="H4_2_gblup_variances_all_11001_12419.rds") +H4_2_gblup_variances_all=c(H4_2_gblup_variances_all_1_1000,H4_2_gblup_variances_all_1001_2000,H4_2_gblup_variances_all_2001_3000,H4_2_gblup_variances_all_3001_4000,H4_2_gblup_variances_all_4001_5000,H4_2_gblup_variances_all_5001_6000,H4_2_gblup_variances_all_6001_7000,H4_2_gblup_variances_all_7001_8000,H4_2_gblup_variances_all_8001_9000,H4_2_gblup_variances_all_9001_10000,H4_2_gblup_variances_all_10001_11000,H4_2_gblup_variances_all_11001_12419) + +saveRDS(H4_2_gblup_prediction_all,"H4_2_gblup_prediction_all.rds") +saveRDS(H4_2_gblup_variances_all,"H4_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H4_2_gfblup_prediction_all_1_1000=readRDS(file="H4_2_gfblup_prediction_all_1_1000.rds") +H4_2_gfblup_prediction_all_1001_2000=readRDS(file="H4_2_gfblup_prediction_all_1001_2000.rds") +H4_2_gfblup_prediction_all_2001_3000=readRDS(file="H4_2_gfblup_prediction_all_2001_3000.rds") +H4_2_gfblup_prediction_all_3001_4000=readRDS(file="H4_2_gfblup_prediction_all_3001_4000.rds") +H4_2_gfblup_prediction_all_4001_5000=readRDS(file="H4_2_gfblup_prediction_all_4001_5000.rds") +H4_2_gfblup_prediction_all_5001_6000=readRDS(file="H4_2_gfblup_prediction_all_5001_6000.rds") +H4_2_gfblup_prediction_all_6001_7000=readRDS(file="H4_2_gfblup_prediction_all_6001_7000.rds") +H4_2_gfblup_prediction_all_7001_8000=readRDS(file="H4_2_gfblup_prediction_all_7001_8000.rds") +H4_2_gfblup_prediction_all_8001_9000=readRDS(file="H4_2_gfblup_prediction_all_8001_9000.rds") +H4_2_gfblup_prediction_all_9001_10000=readRDS(file="H4_2_gfblup_prediction_all_9001_10000.rds") +H4_2_gfblup_prediction_all_10001_11000=readRDS(file="H4_2_gfblup_prediction_all_10001_11000.rds") +H4_2_gfblup_prediction_all_11001_12419=readRDS(file="H4_2_gfblup_prediction_all_11001_12419.rds") + +H4_2_gfblup_variances_all_1_1000=readRDS(file="H4_2_gfblup_variances_all_1_1000.rds") +H4_2_gfblup_variances_all_1001_2000=readRDS(file="H4_2_gfblup_variances_all_1001_2000.rds") +H4_2_gfblup_variances_all_2001_3000=readRDS(file="H4_2_gfblup_variances_all_2001_3000.rds") +H4_2_gfblup_variances_all_3001_4000=readRDS(file="H4_2_gfblup_variances_all_3001_4000.rds") +H4_2_gfblup_variances_all_4001_5000=readRDS(file="H4_2_gfblup_variances_all_4001_5000.rds") +H4_2_gfblup_variances_all_5001_6000=readRDS(file="H4_2_gfblup_variances_all_5001_6000.rds") +H4_2_gfblup_variances_all_6001_7000=readRDS(file="H4_2_gfblup_variances_all_6001_7000.rds") +H4_2_gfblup_variances_all_7001_8000=readRDS(file="H4_2_gfblup_variances_all_7001_8000.rds") +H4_2_gfblup_variances_all_8001_9000=readRDS(file="H4_2_gfblup_variances_all_8001_9000.rds") +H4_2_gfblup_variances_all_9001_10000=readRDS(file="H4_2_gfblup_variances_all_9001_10000.rds") +H4_2_gfblup_variances_all_10001_11000=readRDS(file="H4_2_gfblup_variances_all_10001_11000.rds") +H4_2_gfblup_variances_all_11001_12419=readRDS(file="H4_2_gfblup_variances_all_11001_12419.rds") + +cycles=length(H4_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H4_2_gfblup_variances_all=rep(list(list()),cycles) +H4_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_1_1000[[r]]) + H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_1001_2000[[r]]) + H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_2001_3000[[r]]) + H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_3001_4000[[r]]) + H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_4001_5000[[r]]) + H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_5001_6000[[r]]) + H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_6001_7000[[r]]) + H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_7001_8000[[r]]) + H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_8001_9000[[r]]) + H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_9001_10000[[r]]) + H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_10001_11000[[r]]) + H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_11001_12419[[r]]) + + H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_1_1000[[r]]) + H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_1001_2000[[r]]) + H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_2001_3000[[r]]) + H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_3001_4000[[r]]) + H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_4001_5000[[r]]) + H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_5001_6000[[r]]) + H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_6001_7000[[r]]) + H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_7001_8000[[r]]) + H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_8001_9000[[r]]) + H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_9001_10000[[r]]) + H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_10001_11000[[r]]) + H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(H4_2_gfblup_prediction_all,"H4_2_gfblup_prediction_all.rds") +saveRDS(H4_2_gfblup_variances_all,"H4_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H4_3_gblup_prediction_all_1_1000=readRDS(file="H4_3_gblup_prediction_all_1_1000.rds") +H4_3_gblup_prediction_all_1001_2000=readRDS(file="H4_3_gblup_prediction_all_1001_2000.rds") +H4_3_gblup_prediction_all_2001_3000=readRDS(file="H4_3_gblup_prediction_all_2001_3000.rds") +H4_3_gblup_prediction_all_3001_4000=readRDS(file="H4_3_gblup_prediction_all_3001_4000.rds") +H4_3_gblup_prediction_all_4001_5000=readRDS(file="H4_3_gblup_prediction_all_4001_5000.rds") +H4_3_gblup_prediction_all_5001_6000=readRDS(file="H4_3_gblup_prediction_all_5001_6000.rds") +H4_3_gblup_prediction_all_6001_7000=readRDS(file="H4_3_gblup_prediction_all_6001_7000.rds") +H4_3_gblup_prediction_all_7001_8000=readRDS(file="H4_3_gblup_prediction_all_7001_8000.rds") +H4_3_gblup_prediction_all_8001_9000=readRDS(file="H4_3_gblup_prediction_all_8001_9000.rds") +H4_3_gblup_prediction_all_9001_10000=readRDS(file="H4_3_gblup_prediction_all_9001_10000.rds") +H4_3_gblup_prediction_all_10001_11000=readRDS(file="H4_3_gblup_prediction_all_10001_11000.rds") +H4_3_gblup_prediction_all_11001_12419=readRDS(file="H4_3_gblup_prediction_all_11001_12419.rds") +H4_3_gblup_prediction_all=c(H4_3_gblup_prediction_all_1_1000,H4_3_gblup_prediction_all_1001_2000,H4_3_gblup_prediction_all_2001_3000,H4_3_gblup_prediction_all_3001_4000,H4_3_gblup_prediction_all_4001_5000,H4_3_gblup_prediction_all_5001_6000,H4_3_gblup_prediction_all_6001_7000,H4_3_gblup_prediction_all_7001_8000,H4_3_gblup_prediction_all_8001_9000,H4_3_gblup_prediction_all_9001_10000,H4_3_gblup_prediction_all_10001_11000,H4_3_gblup_prediction_all_11001_12419) + +H4_3_gblup_variances_all_1_1000=readRDS(file="H4_3_gblup_variances_all_1_1000.rds") +H4_3_gblup_variances_all_1001_2000=readRDS(file="H4_3_gblup_variances_all_1001_2000.rds") +H4_3_gblup_variances_all_2001_3000=readRDS(file="H4_3_gblup_variances_all_2001_3000.rds") +H4_3_gblup_variances_all_3001_4000=readRDS(file="H4_3_gblup_variances_all_3001_4000.rds") +H4_3_gblup_variances_all_4001_5000=readRDS(file="H4_3_gblup_variances_all_4001_5000.rds") +H4_3_gblup_variances_all_5001_6000=readRDS(file="H4_3_gblup_variances_all_5001_6000.rds") +H4_3_gblup_variances_all_6001_7000=readRDS(file="H4_3_gblup_variances_all_6001_7000.rds") +H4_3_gblup_variances_all_7001_8000=readRDS(file="H4_3_gblup_variances_all_7001_8000.rds") +H4_3_gblup_variances_all_8001_9000=readRDS(file="H4_3_gblup_variances_all_8001_9000.rds") +H4_3_gblup_variances_all_9001_10000=readRDS(file="H4_3_gblup_variances_all_9001_10000.rds") +H4_3_gblup_variances_all_10001_11000=readRDS(file="H4_3_gblup_variances_all_10001_11000.rds") +H4_3_gblup_variances_all_11001_12419=readRDS(file="H4_3_gblup_variances_all_11001_12419.rds") +H4_3_gblup_variances_all=c(H4_3_gblup_variances_all_1_1000,H4_3_gblup_variances_all_1001_2000,H4_3_gblup_variances_all_2001_3000,H4_3_gblup_variances_all_3001_4000,H4_3_gblup_variances_all_4001_5000,H4_3_gblup_variances_all_5001_6000,H4_3_gblup_variances_all_6001_7000,H4_3_gblup_variances_all_7001_8000,H4_3_gblup_variances_all_8001_9000,H4_3_gblup_variances_all_9001_10000,H4_3_gblup_variances_all_10001_11000,H4_3_gblup_variances_all_11001_12419) + +saveRDS(H4_3_gblup_prediction_all,"H4_3_gblup_prediction_all.rds") +saveRDS(H4_3_gblup_variances_all,"H4_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H4_3_gfblup_prediction_all_1_1000=readRDS(file="H4_3_gfblup_prediction_all_1_1000.rds") +H4_3_gfblup_prediction_all_1001_2000=readRDS(file="H4_3_gfblup_prediction_all_1001_2000.rds") +H4_3_gfblup_prediction_all_2001_3000=readRDS(file="H4_3_gfblup_prediction_all_2001_3000.rds") +H4_3_gfblup_prediction_all_3001_4000=readRDS(file="H4_3_gfblup_prediction_all_3001_4000.rds") +H4_3_gfblup_prediction_all_4001_5000=readRDS(file="H4_3_gfblup_prediction_all_4001_5000.rds") +H4_3_gfblup_prediction_all_5001_6000=readRDS(file="H4_3_gfblup_prediction_all_5001_6000.rds") +H4_3_gfblup_prediction_all_6001_7000=readRDS(file="H4_3_gfblup_prediction_all_6001_7000.rds") +H4_3_gfblup_prediction_all_7001_8000=readRDS(file="H4_3_gfblup_prediction_all_7001_8000.rds") +H4_3_gfblup_prediction_all_8001_9000=readRDS(file="H4_3_gfblup_prediction_all_8001_9000.rds") +H4_3_gfblup_prediction_all_9001_10000=readRDS(file="H4_3_gfblup_prediction_all_9001_10000.rds") +H4_3_gfblup_prediction_all_10001_11000=readRDS(file="H4_3_gfblup_prediction_all_10001_11000.rds") +H4_3_gfblup_prediction_all_11001_12419=readRDS(file="H4_3_gfblup_prediction_all_11001_12419.rds") + +H4_3_gfblup_variances_all_1_1000=readRDS(file="H4_3_gfblup_variances_all_1_1000.rds") +H4_3_gfblup_variances_all_1001_2000=readRDS(file="H4_3_gfblup_variances_all_1001_2000.rds") +H4_3_gfblup_variances_all_2001_3000=readRDS(file="H4_3_gfblup_variances_all_2001_3000.rds") +H4_3_gfblup_variances_all_3001_4000=readRDS(file="H4_3_gfblup_variances_all_3001_4000.rds") +H4_3_gfblup_variances_all_4001_5000=readRDS(file="H4_3_gfblup_variances_all_4001_5000.rds") +H4_3_gfblup_variances_all_5001_6000=readRDS(file="H4_3_gfblup_variances_all_5001_6000.rds") +H4_3_gfblup_variances_all_6001_7000=readRDS(file="H4_3_gfblup_variances_all_6001_7000.rds") +H4_3_gfblup_variances_all_7001_8000=readRDS(file="H4_3_gfblup_variances_all_7001_8000.rds") +H4_3_gfblup_variances_all_8001_9000=readRDS(file="H4_3_gfblup_variances_all_8001_9000.rds") +H4_3_gfblup_variances_all_9001_10000=readRDS(file="H4_3_gfblup_variances_all_9001_10000.rds") +H4_3_gfblup_variances_all_10001_11000=readRDS(file="H4_3_gfblup_variances_all_10001_11000.rds") +H4_3_gfblup_variances_all_11001_12419=readRDS(file="H4_3_gfblup_variances_all_11001_12419.rds") + +cycles=length(H4_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H4_3_gfblup_variances_all=rep(list(list()),cycles) +H4_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_1_1000[[r]]) + H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_1001_2000[[r]]) + H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_2001_3000[[r]]) + H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_3001_4000[[r]]) + H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_4001_5000[[r]]) + H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_5001_6000[[r]]) + H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_6001_7000[[r]]) + H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_7001_8000[[r]]) + H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_8001_9000[[r]]) + H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_9001_10000[[r]]) + H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_10001_11000[[r]]) + H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_11001_12419[[r]]) + + H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_1_1000[[r]]) + H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_1001_2000[[r]]) + H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_2001_3000[[r]]) + H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_3001_4000[[r]]) + H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_4001_5000[[r]]) + H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_5001_6000[[r]]) + H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_6001_7000[[r]]) + H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_7001_8000[[r]]) + H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_8001_9000[[r]]) + H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_9001_10000[[r]]) + H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_10001_11000[[r]]) + H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_11001_12419[[r]]) +} + +saveRDS(H4_3_gfblup_prediction_all,"H4_3_gfblup_prediction_all.rds") +saveRDS(H4_3_gfblup_variances_all,"H4_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/code/using_COEX/psii/gblup_vs_gfblup_using_coexpression_analysis1.R b/code/using_COEX/psii/gblup_vs_gfblup_using_coexpression_analysis1.R index cdf3923d9bb01f25b7cf0e945b66eb3d159a0ac8..a6f69d97d8f1d822be5c874f9d807e79f97fba49 100644 --- a/code/using_COEX/psii/gblup_vs_gfblup_using_coexpression_analysis1.R +++ b/code/using_COEX/psii/gblup_vs_gfblup_using_coexpression_analysis1.R @@ -2,11 +2,27 @@ ################################################################################################################################## # A N A L Y S I S ################################################################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_COEX/psii/8fold/") - -all_coexpression_clusters <-as.data.frame(read.table(file ="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/ath_gene_clusters.txt", header=TRUE, sep="",strip.white=TRUE)) -coex_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/coex_markers_number.rds") -coex_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/coexpression/coex_markers.rds") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} +setwd(paste0(wdir,"/",wd,"/8fold/")); +################################################################################################################################## +all_coexpression_clusters <-as.data.frame(read.table(file ="../data/priors/coexpression/ath_gene_clusters.txt", header=TRUE, sep="",strip.white=TRUE)) +coex_markers_number=readRDS(file="../data/priors/coexpression/coex_markers_number.rds") +coex_markers=readRDS(file="../data/priors/coexpression/coex_markers.rds") ################################################################################################################################### H4_3_gblup_variances_all=readRDS(file="./H4_3_gblup_variances_all.rds") H4_3_gblup_prediction_all=readRDS(file="./H4_3_gblup_prediction_all.rds") diff --git a/code/using_COEX/run_models.R b/code/using_COEX/run_models.R index a53cc2a1333d5ed6c2efb57a5f5ca14055c6008a..48b1b1d4fa2aaef09b11a072206ecf6cb4ff9db9 100644 --- a/code/using_COEX/run_models.R +++ b/code/using_COEX/run_models.R @@ -1,4 +1,23 @@ -cd /mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_COEX +################################################################################################################################## +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} +setwd(paste0(wdir,"/",wd)); +################################################################################################################################## + Rscript psii/H1_1_1_1000.R Rscript psii/H1_1_10001_11000.R Rscript psii/H1_1_1001_2000.R @@ -823,4 +842,4 @@ Rscript pla/T20_2_8001_9000.R Rscript pla/T20_2_9001_10000.R -Rscript psii/8fold/combine.R +Rscript pla/8fold/combine.R diff --git a/code/using_GO/pla/8fold/combine.R b/code/using_GO/pla/8fold/combine.R new file mode 100644 index 0000000000000000000000000000000000000000..0be7b87abb9f64a95a955fd89bc21f3f55a26efd --- /dev/null +++ b/code/using_GO/pla/8fold/combine.R @@ -0,0 +1,3418 @@ +################################################################################################################################## +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} +setwd(paste0(wdir,"/",wd)); +################################################################################################################################## +T14_1_gblup_prediction_all_1_1000=readRDS(file="T14_1_gblup_prediction_all_1_1000.rds") +T14_1_gblup_prediction_all_1001_2000=readRDS(file="T14_1_gblup_prediction_all_1001_2000.rds") +T14_1_gblup_prediction_all_2001_3000=readRDS(file="T14_1_gblup_prediction_all_2001_3000.rds") +T14_1_gblup_prediction_all_3001_4000=readRDS(file="T14_1_gblup_prediction_all_3001_4000.rds") +T14_1_gblup_prediction_all_4001_5000=readRDS(file="T14_1_gblup_prediction_all_4001_5000.rds") +T14_1_gblup_prediction_all_5001_6000=readRDS(file="T14_1_gblup_prediction_all_5001_6000.rds") +T14_1_gblup_prediction_all_6001_7297=readRDS(file="T14_1_gblup_prediction_all_6001_7297.rds") +T14_1_gblup_prediction_all=c(T14_1_gblup_prediction_all_1_1000,T14_1_gblup_prediction_all_1001_2000,T14_1_gblup_prediction_all_2001_3000,T14_1_gblup_prediction_all_3001_4000,T14_1_gblup_prediction_all_4001_5000,T14_1_gblup_prediction_all_5001_6000,T14_1_gblup_prediction_all_6001_7297) + +T14_1_gblup_variances_all_1_1000=readRDS(file="T14_1_gblup_variances_all_1_1000.rds") +T14_1_gblup_variances_all_1001_2000=readRDS(file="T14_1_gblup_variances_all_1001_2000.rds") +T14_1_gblup_variances_all_2001_3000=readRDS(file="T14_1_gblup_variances_all_2001_3000.rds") +T14_1_gblup_variances_all_3001_4000=readRDS(file="T14_1_gblup_variances_all_3001_4000.rds") +T14_1_gblup_variances_all_4001_5000=readRDS(file="T14_1_gblup_variances_all_4001_5000.rds") +T14_1_gblup_variances_all_5001_6000=readRDS(file="T14_1_gblup_variances_all_5001_6000.rds") +T14_1_gblup_variances_all_6001_7297=readRDS(file="T14_1_gblup_variances_all_6001_7297.rds") +T14_1_gblup_variances_all=c(T14_1_gblup_variances_all_1_1000,T14_1_gblup_variances_all_1001_2000,T14_1_gblup_variances_all_2001_3000,T14_1_gblup_variances_all_3001_4000,T14_1_gblup_variances_all_4001_5000,T14_1_gblup_variances_all_5001_6000,T14_1_gblup_variances_all_6001_7297) + +saveRDS(T14_1_gblup_prediction_all,"T14_1_gblup_prediction_all.rds") +saveRDS(T14_1_gblup_variances_all,"T14_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_1_gfblup_prediction_all_1_1000=readRDS(file="T14_1_gfblup_prediction_all_1_1000.rds") +T14_1_gfblup_prediction_all_1001_2000=readRDS(file="T14_1_gfblup_prediction_all_1001_2000.rds") +T14_1_gfblup_prediction_all_2001_3000=readRDS(file="T14_1_gfblup_prediction_all_2001_3000.rds") +T14_1_gfblup_prediction_all_3001_4000=readRDS(file="T14_1_gfblup_prediction_all_3001_4000.rds") +T14_1_gfblup_prediction_all_4001_5000=readRDS(file="T14_1_gfblup_prediction_all_4001_5000.rds") +T14_1_gfblup_prediction_all_5001_6000=readRDS(file="T14_1_gfblup_prediction_all_5001_6000.rds") +T14_1_gfblup_prediction_all_6001_7297=readRDS(file="T14_1_gfblup_prediction_all_6001_7297.rds") + +T14_1_gfblup_variances_all_1_1000=readRDS(file="T14_1_gfblup_variances_all_1_1000.rds") +T14_1_gfblup_variances_all_1001_2000=readRDS(file="T14_1_gfblup_variances_all_1001_2000.rds") +T14_1_gfblup_variances_all_2001_3000=readRDS(file="T14_1_gfblup_variances_all_2001_3000.rds") +T14_1_gfblup_variances_all_3001_4000=readRDS(file="T14_1_gfblup_variances_all_3001_4000.rds") +T14_1_gfblup_variances_all_4001_5000=readRDS(file="T14_1_gfblup_variances_all_4001_5000.rds") +T14_1_gfblup_variances_all_5001_6000=readRDS(file="T14_1_gfblup_variances_all_5001_6000.rds") +T14_1_gfblup_variances_all_6001_7297=readRDS(file="T14_1_gfblup_variances_all_6001_7297.rds") + +cycles=length(T14_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T14_1_gfblup_variances_all=rep(list(list()),cycles) +T14_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_1_1000[[r]]) + T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_1001_2000[[r]]) + T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_2001_3000[[r]]) + T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_3001_4000[[r]]) + T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_4001_5000[[r]]) + T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_5001_6000[[r]]) + T14_1_gfblup_prediction_all[[r]]<-c(T14_1_gfblup_prediction_all[[r]],T14_1_gfblup_prediction_all_6001_7297[[r]]) + + T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_1_1000[[r]]) + T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_1001_2000[[r]]) + T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_2001_3000[[r]]) + T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_3001_4000[[r]]) + T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_4001_5000[[r]]) + T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_5001_6000[[r]]) + T14_1_gfblup_variances_all[[r]]<-c(T14_1_gfblup_variances_all[[r]],T14_1_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T14_1_gfblup_prediction_all,"T14_1_gfblup_prediction_all.rds") +saveRDS(T14_1_gfblup_variances_all,"T14_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_2_gblup_prediction_all_1_1000=readRDS(file="T14_2_gblup_prediction_all_1_1000.rds") +T14_2_gblup_prediction_all_1001_2000=readRDS(file="T14_2_gblup_prediction_all_1001_2000.rds") +T14_2_gblup_prediction_all_2001_3000=readRDS(file="T14_2_gblup_prediction_all_2001_3000.rds") +T14_2_gblup_prediction_all_3001_4000=readRDS(file="T14_2_gblup_prediction_all_3001_4000.rds") +T14_2_gblup_prediction_all_4001_5000=readRDS(file="T14_2_gblup_prediction_all_4001_5000.rds") +T14_2_gblup_prediction_all_5001_6000=readRDS(file="T14_2_gblup_prediction_all_5001_6000.rds") +T14_2_gblup_prediction_all_6001_7297=readRDS(file="T14_2_gblup_prediction_all_6001_7297.rds") +T14_2_gblup_prediction_all=c(T14_2_gblup_prediction_all_1_1000,T14_2_gblup_prediction_all_1001_2000,T14_2_gblup_prediction_all_2001_3000,T14_2_gblup_prediction_all_3001_4000,T14_2_gblup_prediction_all_4001_5000,T14_2_gblup_prediction_all_5001_6000,T14_2_gblup_prediction_all_6001_7297) + +T14_2_gblup_variances_all_1_1000=readRDS(file="T14_2_gblup_variances_all_1_1000.rds") +T14_2_gblup_variances_all_1001_2000=readRDS(file="T14_2_gblup_variances_all_1001_2000.rds") +T14_2_gblup_variances_all_2001_3000=readRDS(file="T14_2_gblup_variances_all_2001_3000.rds") +T14_2_gblup_variances_all_3001_4000=readRDS(file="T14_2_gblup_variances_all_3001_4000.rds") +T14_2_gblup_variances_all_4001_5000=readRDS(file="T14_2_gblup_variances_all_4001_5000.rds") +T14_2_gblup_variances_all_5001_6000=readRDS(file="T14_2_gblup_variances_all_5001_6000.rds") +T14_2_gblup_variances_all_6001_7297=readRDS(file="T14_2_gblup_variances_all_6001_7297.rds") +T14_2_gblup_variances_all=c(T14_2_gblup_variances_all_1_1000,T14_2_gblup_variances_all_1001_2000,T14_2_gblup_variances_all_2001_3000,T14_2_gblup_variances_all_3001_4000,T14_2_gblup_variances_all_4001_5000,T14_2_gblup_variances_all_5001_6000,T14_2_gblup_variances_all_6001_7297) + +saveRDS(T14_2_gblup_prediction_all,"T14_2_gblup_prediction_all.rds") +saveRDS(T14_2_gblup_variances_all,"T14_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_2_gfblup_prediction_all_1_1000=readRDS(file="T14_2_gfblup_prediction_all_1_1000.rds") +T14_2_gfblup_prediction_all_1001_2000=readRDS(file="T14_2_gfblup_prediction_all_1001_2000.rds") +T14_2_gfblup_prediction_all_2001_3000=readRDS(file="T14_2_gfblup_prediction_all_2001_3000.rds") +T14_2_gfblup_prediction_all_3001_4000=readRDS(file="T14_2_gfblup_prediction_all_3001_4000.rds") +T14_2_gfblup_prediction_all_4001_5000=readRDS(file="T14_2_gfblup_prediction_all_4001_5000.rds") +T14_2_gfblup_prediction_all_5001_6000=readRDS(file="T14_2_gfblup_prediction_all_5001_6000.rds") +T14_2_gfblup_prediction_all_6001_7297=readRDS(file="T14_2_gfblup_prediction_all_6001_7297.rds") + +T14_2_gfblup_variances_all_1_1000=readRDS(file="T14_2_gfblup_variances_all_1_1000.rds") +T14_2_gfblup_variances_all_1001_2000=readRDS(file="T14_2_gfblup_variances_all_1001_2000.rds") +T14_2_gfblup_variances_all_2001_3000=readRDS(file="T14_2_gfblup_variances_all_2001_3000.rds") +T14_2_gfblup_variances_all_3001_4000=readRDS(file="T14_2_gfblup_variances_all_3001_4000.rds") +T14_2_gfblup_variances_all_4001_5000=readRDS(file="T14_2_gfblup_variances_all_4001_5000.rds") +T14_2_gfblup_variances_all_5001_6000=readRDS(file="T14_2_gfblup_variances_all_5001_6000.rds") +T14_2_gfblup_variances_all_6001_7297=readRDS(file="T14_2_gfblup_variances_all_6001_7297.rds") + +cycles=length(T14_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T14_2_gfblup_variances_all=rep(list(list()),cycles) +T14_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_1_1000[[r]]) + T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_1001_2000[[r]]) + T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_2001_3000[[r]]) + T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_3001_4000[[r]]) + T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_4001_5000[[r]]) + T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_5001_6000[[r]]) + T14_2_gfblup_prediction_all[[r]]<-c(T14_2_gfblup_prediction_all[[r]],T14_2_gfblup_prediction_all_6001_7297[[r]]) + + T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_1_1000[[r]]) + T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_1001_2000[[r]]) + T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_2001_3000[[r]]) + T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_3001_4000[[r]]) + T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_4001_5000[[r]]) + T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_5001_6000[[r]]) + T14_2_gfblup_variances_all[[r]]<-c(T14_2_gfblup_variances_all[[r]],T14_2_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T14_2_gfblup_prediction_all,"T14_2_gfblup_prediction_all.rds") +saveRDS(T14_2_gfblup_variances_all,"T14_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_3_gblup_prediction_all_1_1000=readRDS(file="T14_3_gblup_prediction_all_1_1000.rds") +T14_3_gblup_prediction_all_1001_2000=readRDS(file="T14_3_gblup_prediction_all_1001_2000.rds") +T14_3_gblup_prediction_all_2001_3000=readRDS(file="T14_3_gblup_prediction_all_2001_3000.rds") +T14_3_gblup_prediction_all_3001_4000=readRDS(file="T14_3_gblup_prediction_all_3001_4000.rds") +T14_3_gblup_prediction_all_4001_5000=readRDS(file="T14_3_gblup_prediction_all_4001_5000.rds") +T14_3_gblup_prediction_all_5001_6000=readRDS(file="T14_3_gblup_prediction_all_5001_6000.rds") +T14_3_gblup_prediction_all_6001_7297=readRDS(file="T14_3_gblup_prediction_all_6001_7297.rds") +T14_3_gblup_prediction_all=c(T14_3_gblup_prediction_all_1_1000,T14_3_gblup_prediction_all_1001_2000,T14_3_gblup_prediction_all_2001_3000,T14_3_gblup_prediction_all_3001_4000,T14_3_gblup_prediction_all_4001_5000,T14_3_gblup_prediction_all_5001_6000,T14_3_gblup_prediction_all_6001_7297) + +T14_3_gblup_variances_all_1_1000=readRDS(file="T14_3_gblup_variances_all_1_1000.rds") +T14_3_gblup_variances_all_1001_2000=readRDS(file="T14_3_gblup_variances_all_1001_2000.rds") +T14_3_gblup_variances_all_2001_3000=readRDS(file="T14_3_gblup_variances_all_2001_3000.rds") +T14_3_gblup_variances_all_3001_4000=readRDS(file="T14_3_gblup_variances_all_3001_4000.rds") +T14_3_gblup_variances_all_4001_5000=readRDS(file="T14_3_gblup_variances_all_4001_5000.rds") +T14_3_gblup_variances_all_5001_6000=readRDS(file="T14_3_gblup_variances_all_5001_6000.rds") +T14_3_gblup_variances_all_6001_7297=readRDS(file="T14_3_gblup_variances_all_6001_7297.rds") +T14_3_gblup_variances_all=c(T14_3_gblup_variances_all_1_1000,T14_3_gblup_variances_all_1001_2000,T14_3_gblup_variances_all_2001_3000,T14_3_gblup_variances_all_3001_4000,T14_3_gblup_variances_all_4001_5000,T14_3_gblup_variances_all_5001_6000,T14_3_gblup_variances_all_6001_7297) + +saveRDS(T14_3_gblup_prediction_all,"T14_3_gblup_prediction_all.rds") +saveRDS(T14_3_gblup_variances_all,"T14_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_3_gfblup_prediction_all_1_1000=readRDS(file="T14_3_gfblup_prediction_all_1_1000.rds") +T14_3_gfblup_prediction_all_1001_2000=readRDS(file="T14_3_gfblup_prediction_all_1001_2000.rds") +T14_3_gfblup_prediction_all_2001_3000=readRDS(file="T14_3_gfblup_prediction_all_2001_3000.rds") +T14_3_gfblup_prediction_all_3001_4000=readRDS(file="T14_3_gfblup_prediction_all_3001_4000.rds") +T14_3_gfblup_prediction_all_4001_5000=readRDS(file="T14_3_gfblup_prediction_all_4001_5000.rds") +T14_3_gfblup_prediction_all_5001_6000=readRDS(file="T14_3_gfblup_prediction_all_5001_6000.rds") +T14_3_gfblup_prediction_all_6001_7297=readRDS(file="T14_3_gfblup_prediction_all_6001_7297.rds") + +T14_3_gfblup_variances_all_1_1000=readRDS(file="T14_3_gfblup_variances_all_1_1000.rds") +T14_3_gfblup_variances_all_1001_2000=readRDS(file="T14_3_gfblup_variances_all_1001_2000.rds") +T14_3_gfblup_variances_all_2001_3000=readRDS(file="T14_3_gfblup_variances_all_2001_3000.rds") +T14_3_gfblup_variances_all_3001_4000=readRDS(file="T14_3_gfblup_variances_all_3001_4000.rds") +T14_3_gfblup_variances_all_4001_5000=readRDS(file="T14_3_gfblup_variances_all_4001_5000.rds") +T14_3_gfblup_variances_all_5001_6000=readRDS(file="T14_3_gfblup_variances_all_5001_6000.rds") +T14_3_gfblup_variances_all_6001_7297=readRDS(file="T14_3_gfblup_variances_all_6001_7297.rds") + +cycles=length(T14_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T14_3_gfblup_variances_all=rep(list(list()),cycles) +T14_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_1_1000[[r]]) + T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_1001_2000[[r]]) + T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_2001_3000[[r]]) + T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_3001_4000[[r]]) + T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_4001_5000[[r]]) + T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_5001_6000[[r]]) + T14_3_gfblup_prediction_all[[r]]<-c(T14_3_gfblup_prediction_all[[r]],T14_3_gfblup_prediction_all_6001_7297[[r]]) + + T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_1_1000[[r]]) + T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_1001_2000[[r]]) + T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_2001_3000[[r]]) + T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_3001_4000[[r]]) + T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_4001_5000[[r]]) + T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_5001_6000[[r]]) + T14_3_gfblup_variances_all[[r]]<-c(T14_3_gfblup_variances_all[[r]],T14_3_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T14_3_gfblup_prediction_all,"T14_3_gfblup_prediction_all.rds") +saveRDS(T14_3_gfblup_variances_all,"T14_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_4_gblup_prediction_all_1_1000=readRDS(file="T14_4_gblup_prediction_all_1_1000.rds") +T14_4_gblup_prediction_all_1001_2000=readRDS(file="T14_4_gblup_prediction_all_1001_2000.rds") +T14_4_gblup_prediction_all_2001_3000=readRDS(file="T14_4_gblup_prediction_all_2001_3000.rds") +T14_4_gblup_prediction_all_3001_4000=readRDS(file="T14_4_gblup_prediction_all_3001_4000.rds") +T14_4_gblup_prediction_all_4001_5000=readRDS(file="T14_4_gblup_prediction_all_4001_5000.rds") +T14_4_gblup_prediction_all_5001_6000=readRDS(file="T14_4_gblup_prediction_all_5001_6000.rds") +T14_4_gblup_prediction_all_6001_7297=readRDS(file="T14_4_gblup_prediction_all_6001_7297.rds") +T14_4_gblup_prediction_all=c(T14_4_gblup_prediction_all_1_1000,T14_4_gblup_prediction_all_1001_2000,T14_4_gblup_prediction_all_2001_3000,T14_4_gblup_prediction_all_3001_4000,T14_4_gblup_prediction_all_4001_5000,T14_4_gblup_prediction_all_5001_6000,T14_4_gblup_prediction_all_6001_7297) + +T14_4_gblup_variances_all_1_1000=readRDS(file="T14_4_gblup_variances_all_1_1000.rds") +T14_4_gblup_variances_all_1001_2000=readRDS(file="T14_4_gblup_variances_all_1001_2000.rds") +T14_4_gblup_variances_all_2001_3000=readRDS(file="T14_4_gblup_variances_all_2001_3000.rds") +T14_4_gblup_variances_all_3001_4000=readRDS(file="T14_4_gblup_variances_all_3001_4000.rds") +T14_4_gblup_variances_all_4001_5000=readRDS(file="T14_4_gblup_variances_all_4001_5000.rds") +T14_4_gblup_variances_all_5001_6000=readRDS(file="T14_4_gblup_variances_all_5001_6000.rds") +T14_4_gblup_variances_all_6001_7297=readRDS(file="T14_4_gblup_variances_all_6001_7297.rds") +T14_4_gblup_variances_all=c(T14_4_gblup_variances_all_1_1000,T14_4_gblup_variances_all_1001_2000,T14_4_gblup_variances_all_2001_3000,T14_4_gblup_variances_all_3001_4000,T14_4_gblup_variances_all_4001_5000,T14_4_gblup_variances_all_5001_6000,T14_4_gblup_variances_all_6001_7297) + +saveRDS(T14_4_gblup_prediction_all,"T14_4_gblup_prediction_all.rds") +saveRDS(T14_4_gblup_variances_all,"T14_4_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_4_gfblup_prediction_all_1_1000=readRDS(file="T14_4_gfblup_prediction_all_1_1000.rds") +T14_4_gfblup_prediction_all_1001_2000=readRDS(file="T14_4_gfblup_prediction_all_1001_2000.rds") +T14_4_gfblup_prediction_all_2001_3000=readRDS(file="T14_4_gfblup_prediction_all_2001_3000.rds") +T14_4_gfblup_prediction_all_3001_4000=readRDS(file="T14_4_gfblup_prediction_all_3001_4000.rds") +T14_4_gfblup_prediction_all_4001_5000=readRDS(file="T14_4_gfblup_prediction_all_4001_5000.rds") +T14_4_gfblup_prediction_all_5001_6000=readRDS(file="T14_4_gfblup_prediction_all_5001_6000.rds") +T14_4_gfblup_prediction_all_6001_7297=readRDS(file="T14_4_gfblup_prediction_all_6001_7297.rds") + +T14_4_gfblup_variances_all_1_1000=readRDS(file="T14_4_gfblup_variances_all_1_1000.rds") +T14_4_gfblup_variances_all_1001_2000=readRDS(file="T14_4_gfblup_variances_all_1001_2000.rds") +T14_4_gfblup_variances_all_2001_3000=readRDS(file="T14_4_gfblup_variances_all_2001_3000.rds") +T14_4_gfblup_variances_all_3001_4000=readRDS(file="T14_4_gfblup_variances_all_3001_4000.rds") +T14_4_gfblup_variances_all_4001_5000=readRDS(file="T14_4_gfblup_variances_all_4001_5000.rds") +T14_4_gfblup_variances_all_5001_6000=readRDS(file="T14_4_gfblup_variances_all_5001_6000.rds") +T14_4_gfblup_variances_all_6001_7297=readRDS(file="T14_4_gfblup_variances_all_6001_7297.rds") + +cycles=length(T14_4_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T14_4_gfblup_variances_all=rep(list(list()),cycles) +T14_4_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_1_1000[[r]]) + T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_1001_2000[[r]]) + T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_2001_3000[[r]]) + T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_3001_4000[[r]]) + T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_4001_5000[[r]]) + T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_5001_6000[[r]]) + T14_4_gfblup_prediction_all[[r]]<-c(T14_4_gfblup_prediction_all[[r]],T14_4_gfblup_prediction_all_6001_7297[[r]]) + + T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_1_1000[[r]]) + T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_1001_2000[[r]]) + T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_2001_3000[[r]]) + T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_3001_4000[[r]]) + T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_4001_5000[[r]]) + T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_5001_6000[[r]]) + T14_4_gfblup_variances_all[[r]]<-c(T14_4_gfblup_variances_all[[r]],T14_4_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T14_4_gfblup_prediction_all,"T14_4_gfblup_prediction_all.rds") +saveRDS(T14_4_gfblup_variances_all,"T14_4_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_5_gblup_prediction_all_1_1000=readRDS(file="T14_5_gblup_prediction_all_1_1000.rds") +T14_5_gblup_prediction_all_1001_2000=readRDS(file="T14_5_gblup_prediction_all_1001_2000.rds") +T14_5_gblup_prediction_all_2001_3000=readRDS(file="T14_5_gblup_prediction_all_2001_3000.rds") +T14_5_gblup_prediction_all_3001_4000=readRDS(file="T14_5_gblup_prediction_all_3001_4000.rds") +T14_5_gblup_prediction_all_4001_5000=readRDS(file="T14_5_gblup_prediction_all_4001_5000.rds") +T14_5_gblup_prediction_all_5001_6000=readRDS(file="T14_5_gblup_prediction_all_5001_6000.rds") +T14_5_gblup_prediction_all_6001_7297=readRDS(file="T14_5_gblup_prediction_all_6001_7297.rds") +T14_5_gblup_prediction_all=c(T14_5_gblup_prediction_all_1_1000,T14_5_gblup_prediction_all_1001_2000,T14_5_gblup_prediction_all_2001_3000,T14_5_gblup_prediction_all_3001_4000,T14_5_gblup_prediction_all_4001_5000,T14_5_gblup_prediction_all_5001_6000,T14_5_gblup_prediction_all_6001_7297) + +T14_5_gblup_variances_all_1_1000=readRDS(file="T14_5_gblup_variances_all_1_1000.rds") +T14_5_gblup_variances_all_1001_2000=readRDS(file="T14_5_gblup_variances_all_1001_2000.rds") +T14_5_gblup_variances_all_2001_3000=readRDS(file="T14_5_gblup_variances_all_2001_3000.rds") +T14_5_gblup_variances_all_3001_4000=readRDS(file="T14_5_gblup_variances_all_3001_4000.rds") +T14_5_gblup_variances_all_4001_5000=readRDS(file="T14_5_gblup_variances_all_4001_5000.rds") +T14_5_gblup_variances_all_5001_6000=readRDS(file="T14_5_gblup_variances_all_5001_6000.rds") +T14_5_gblup_variances_all_6001_7297=readRDS(file="T14_5_gblup_variances_all_6001_7297.rds") +T14_5_gblup_variances_all=c(T14_5_gblup_variances_all_1_1000,T14_5_gblup_variances_all_1001_2000,T14_5_gblup_variances_all_2001_3000,T14_5_gblup_variances_all_3001_4000,T14_5_gblup_variances_all_4001_5000,T14_5_gblup_variances_all_5001_6000,T14_5_gblup_variances_all_6001_7297) + +saveRDS(T14_5_gblup_prediction_all,"T14_5_gblup_prediction_all.rds") +saveRDS(T14_5_gblup_variances_all,"T14_5_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_5_gfblup_prediction_all_1_1000=readRDS(file="T14_5_gfblup_prediction_all_1_1000.rds") +T14_5_gfblup_prediction_all_1001_2000=readRDS(file="T14_5_gfblup_prediction_all_1001_2000.rds") +T14_5_gfblup_prediction_all_2001_3000=readRDS(file="T14_5_gfblup_prediction_all_2001_3000.rds") +T14_5_gfblup_prediction_all_3001_4000=readRDS(file="T14_5_gfblup_prediction_all_3001_4000.rds") +T14_5_gfblup_prediction_all_4001_5000=readRDS(file="T14_5_gfblup_prediction_all_4001_5000.rds") +T14_5_gfblup_prediction_all_5001_6000=readRDS(file="T14_5_gfblup_prediction_all_5001_6000.rds") +T14_5_gfblup_prediction_all_6001_7297=readRDS(file="T14_5_gfblup_prediction_all_6001_7297.rds") + +T14_5_gfblup_variances_all_1_1000=readRDS(file="T14_5_gfblup_variances_all_1_1000.rds") +T14_5_gfblup_variances_all_1001_2000=readRDS(file="T14_5_gfblup_variances_all_1001_2000.rds") +T14_5_gfblup_variances_all_2001_3000=readRDS(file="T14_5_gfblup_variances_all_2001_3000.rds") +T14_5_gfblup_variances_all_3001_4000=readRDS(file="T14_5_gfblup_variances_all_3001_4000.rds") +T14_5_gfblup_variances_all_4001_5000=readRDS(file="T14_5_gfblup_variances_all_4001_5000.rds") +T14_5_gfblup_variances_all_5001_6000=readRDS(file="T14_5_gfblup_variances_all_5001_6000.rds") +T14_5_gfblup_variances_all_6001_7297=readRDS(file="T14_5_gfblup_variances_all_6001_7297.rds") + +cycles=length(T14_5_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T14_5_gfblup_variances_all=rep(list(list()),cycles) +T14_5_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_1_1000[[r]]) + T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_1001_2000[[r]]) + T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_2001_3000[[r]]) + T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_3001_4000[[r]]) + T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_4001_5000[[r]]) + T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_5001_6000[[r]]) + T14_5_gfblup_prediction_all[[r]]<-c(T14_5_gfblup_prediction_all[[r]],T14_5_gfblup_prediction_all_6001_7297[[r]]) + + T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_1_1000[[r]]) + T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_1001_2000[[r]]) + T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_2001_3000[[r]]) + T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_3001_4000[[r]]) + T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_4001_5000[[r]]) + T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_5001_6000[[r]]) + T14_5_gfblup_variances_all[[r]]<-c(T14_5_gfblup_variances_all[[r]],T14_5_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T14_5_gfblup_prediction_all,"T14_5_gfblup_prediction_all.rds") +saveRDS(T14_5_gfblup_variances_all,"T14_5_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_6_gblup_prediction_all_1_1000=readRDS(file="T14_6_gblup_prediction_all_1_1000.rds") +T14_6_gblup_prediction_all_1001_2000=readRDS(file="T14_6_gblup_prediction_all_1001_2000.rds") +T14_6_gblup_prediction_all_2001_3000=readRDS(file="T14_6_gblup_prediction_all_2001_3000.rds") +T14_6_gblup_prediction_all_3001_4000=readRDS(file="T14_6_gblup_prediction_all_3001_4000.rds") +T14_6_gblup_prediction_all_4001_5000=readRDS(file="T14_6_gblup_prediction_all_4001_5000.rds") +T14_6_gblup_prediction_all_5001_6000=readRDS(file="T14_6_gblup_prediction_all_5001_6000.rds") +T14_6_gblup_prediction_all_6001_7297=readRDS(file="T14_6_gblup_prediction_all_6001_7297.rds") +T14_6_gblup_prediction_all=c(T14_6_gblup_prediction_all_1_1000,T14_6_gblup_prediction_all_1001_2000,T14_6_gblup_prediction_all_2001_3000,T14_6_gblup_prediction_all_3001_4000,T14_6_gblup_prediction_all_4001_5000,T14_6_gblup_prediction_all_5001_6000,T14_6_gblup_prediction_all_6001_7297) + +T14_6_gblup_variances_all_1_1000=readRDS(file="T14_6_gblup_variances_all_1_1000.rds") +T14_6_gblup_variances_all_1001_2000=readRDS(file="T14_6_gblup_variances_all_1001_2000.rds") +T14_6_gblup_variances_all_2001_3000=readRDS(file="T14_6_gblup_variances_all_2001_3000.rds") +T14_6_gblup_variances_all_3001_4000=readRDS(file="T14_6_gblup_variances_all_3001_4000.rds") +T14_6_gblup_variances_all_4001_5000=readRDS(file="T14_6_gblup_variances_all_4001_5000.rds") +T14_6_gblup_variances_all_5001_6000=readRDS(file="T14_6_gblup_variances_all_5001_6000.rds") +T14_6_gblup_variances_all_6001_7297=readRDS(file="T14_6_gblup_variances_all_6001_7297.rds") +T14_6_gblup_variances_all=c(T14_6_gblup_variances_all_1_1000,T14_6_gblup_variances_all_1001_2000,T14_6_gblup_variances_all_2001_3000,T14_6_gblup_variances_all_3001_4000,T14_6_gblup_variances_all_4001_5000,T14_6_gblup_variances_all_5001_6000,T14_6_gblup_variances_all_6001_7297) + +saveRDS(T14_6_gblup_prediction_all,"T14_6_gblup_prediction_all.rds") +saveRDS(T14_6_gblup_variances_all,"T14_6_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_6_gfblup_prediction_all_1_1000=readRDS(file="T14_6_gfblup_prediction_all_1_1000.rds") +T14_6_gfblup_prediction_all_1001_2000=readRDS(file="T14_6_gfblup_prediction_all_1001_2000.rds") +T14_6_gfblup_prediction_all_2001_3000=readRDS(file="T14_6_gfblup_prediction_all_2001_3000.rds") +T14_6_gfblup_prediction_all_3001_4000=readRDS(file="T14_6_gfblup_prediction_all_3001_4000.rds") +T14_6_gfblup_prediction_all_4001_5000=readRDS(file="T14_6_gfblup_prediction_all_4001_5000.rds") +T14_6_gfblup_prediction_all_5001_6000=readRDS(file="T14_6_gfblup_prediction_all_5001_6000.rds") +T14_6_gfblup_prediction_all_6001_7297=readRDS(file="T14_6_gfblup_prediction_all_6001_7297.rds") + +T14_6_gfblup_variances_all_1_1000=readRDS(file="T14_6_gfblup_variances_all_1_1000.rds") +T14_6_gfblup_variances_all_1001_2000=readRDS(file="T14_6_gfblup_variances_all_1001_2000.rds") +T14_6_gfblup_variances_all_2001_3000=readRDS(file="T14_6_gfblup_variances_all_2001_3000.rds") +T14_6_gfblup_variances_all_3001_4000=readRDS(file="T14_6_gfblup_variances_all_3001_4000.rds") +T14_6_gfblup_variances_all_4001_5000=readRDS(file="T14_6_gfblup_variances_all_4001_5000.rds") +T14_6_gfblup_variances_all_5001_6000=readRDS(file="T14_6_gfblup_variances_all_5001_6000.rds") +T14_6_gfblup_variances_all_6001_7297=readRDS(file="T14_6_gfblup_variances_all_6001_7297.rds") + +cycles=length(T14_6_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T14_6_gfblup_variances_all=rep(list(list()),cycles) +T14_6_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_1_1000[[r]]) + T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_1001_2000[[r]]) + T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_2001_3000[[r]]) + T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_3001_4000[[r]]) + T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_4001_5000[[r]]) + T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_5001_6000[[r]]) + T14_6_gfblup_prediction_all[[r]]<-c(T14_6_gfblup_prediction_all[[r]],T14_6_gfblup_prediction_all_6001_7297[[r]]) + + T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_1_1000[[r]]) + T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_1001_2000[[r]]) + T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_2001_3000[[r]]) + T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_3001_4000[[r]]) + T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_4001_5000[[r]]) + T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_5001_6000[[r]]) + T14_6_gfblup_variances_all[[r]]<-c(T14_6_gfblup_variances_all[[r]],T14_6_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T14_6_gfblup_prediction_all,"T14_6_gfblup_prediction_all.rds") +saveRDS(T14_6_gfblup_variances_all,"T14_6_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_7_gblup_prediction_all_1_1000=readRDS(file="T14_7_gblup_prediction_all_1_1000.rds") +T14_7_gblup_prediction_all_1001_2000=readRDS(file="T14_7_gblup_prediction_all_1001_2000.rds") +T14_7_gblup_prediction_all_2001_3000=readRDS(file="T14_7_gblup_prediction_all_2001_3000.rds") +T14_7_gblup_prediction_all_3001_4000=readRDS(file="T14_7_gblup_prediction_all_3001_4000.rds") +T14_7_gblup_prediction_all_4001_5000=readRDS(file="T14_7_gblup_prediction_all_4001_5000.rds") +T14_7_gblup_prediction_all_5001_6000=readRDS(file="T14_7_gblup_prediction_all_5001_6000.rds") +T14_7_gblup_prediction_all_6001_7297=readRDS(file="T14_7_gblup_prediction_all_6001_7297.rds") +T14_7_gblup_prediction_all=c(T14_7_gblup_prediction_all_1_1000,T14_7_gblup_prediction_all_1001_2000,T14_7_gblup_prediction_all_2001_3000,T14_7_gblup_prediction_all_3001_4000,T14_7_gblup_prediction_all_4001_5000,T14_7_gblup_prediction_all_5001_6000,T14_7_gblup_prediction_all_6001_7297) + +T14_7_gblup_variances_all_1_1000=readRDS(file="T14_7_gblup_variances_all_1_1000.rds") +T14_7_gblup_variances_all_1001_2000=readRDS(file="T14_7_gblup_variances_all_1001_2000.rds") +T14_7_gblup_variances_all_2001_3000=readRDS(file="T14_7_gblup_variances_all_2001_3000.rds") +T14_7_gblup_variances_all_3001_4000=readRDS(file="T14_7_gblup_variances_all_3001_4000.rds") +T14_7_gblup_variances_all_4001_5000=readRDS(file="T14_7_gblup_variances_all_4001_5000.rds") +T14_7_gblup_variances_all_5001_6000=readRDS(file="T14_7_gblup_variances_all_5001_6000.rds") +T14_7_gblup_variances_all_6001_7297=readRDS(file="T14_7_gblup_variances_all_6001_7297.rds") +T14_7_gblup_variances_all=c(T14_7_gblup_variances_all_1_1000,T14_7_gblup_variances_all_1001_2000,T14_7_gblup_variances_all_2001_3000,T14_7_gblup_variances_all_3001_4000,T14_7_gblup_variances_all_4001_5000,T14_7_gblup_variances_all_5001_6000,T14_7_gblup_variances_all_6001_7297) + +saveRDS(T14_7_gblup_prediction_all,"T14_7_gblup_prediction_all.rds") +saveRDS(T14_7_gblup_variances_all,"T14_7_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_7_gfblup_prediction_all_1_1000=readRDS(file="T14_7_gfblup_prediction_all_1_1000.rds") +T14_7_gfblup_prediction_all_1001_2000=readRDS(file="T14_7_gfblup_prediction_all_1001_2000.rds") +T14_7_gfblup_prediction_all_2001_3000=readRDS(file="T14_7_gfblup_prediction_all_2001_3000.rds") +T14_7_gfblup_prediction_all_3001_4000=readRDS(file="T14_7_gfblup_prediction_all_3001_4000.rds") +T14_7_gfblup_prediction_all_4001_5000=readRDS(file="T14_7_gfblup_prediction_all_4001_5000.rds") +T14_7_gfblup_prediction_all_5001_6000=readRDS(file="T14_7_gfblup_prediction_all_5001_6000.rds") +T14_7_gfblup_prediction_all_6001_7297=readRDS(file="T14_7_gfblup_prediction_all_6001_7297.rds") + +T14_7_gfblup_variances_all_1_1000=readRDS(file="T14_7_gfblup_variances_all_1_1000.rds") +T14_7_gfblup_variances_all_1001_2000=readRDS(file="T14_7_gfblup_variances_all_1001_2000.rds") +T14_7_gfblup_variances_all_2001_3000=readRDS(file="T14_7_gfblup_variances_all_2001_3000.rds") +T14_7_gfblup_variances_all_3001_4000=readRDS(file="T14_7_gfblup_variances_all_3001_4000.rds") +T14_7_gfblup_variances_all_4001_5000=readRDS(file="T14_7_gfblup_variances_all_4001_5000.rds") +T14_7_gfblup_variances_all_5001_6000=readRDS(file="T14_7_gfblup_variances_all_5001_6000.rds") +T14_7_gfblup_variances_all_6001_7297=readRDS(file="T14_7_gfblup_variances_all_6001_7297.rds") + +cycles=length(T14_7_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T14_7_gfblup_variances_all=rep(list(list()),cycles) +T14_7_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_1_1000[[r]]) + T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_1001_2000[[r]]) + T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_2001_3000[[r]]) + T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_3001_4000[[r]]) + T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_4001_5000[[r]]) + T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_5001_6000[[r]]) + T14_7_gfblup_prediction_all[[r]]<-c(T14_7_gfblup_prediction_all[[r]],T14_7_gfblup_prediction_all_6001_7297[[r]]) + + T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_1_1000[[r]]) + T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_1001_2000[[r]]) + T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_2001_3000[[r]]) + T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_3001_4000[[r]]) + T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_4001_5000[[r]]) + T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_5001_6000[[r]]) + T14_7_gfblup_variances_all[[r]]<-c(T14_7_gfblup_variances_all[[r]],T14_7_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T14_7_gfblup_prediction_all,"T14_7_gfblup_prediction_all.rds") +saveRDS(T14_7_gfblup_variances_all,"T14_7_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_8_gblup_prediction_all_1_1000=readRDS(file="T14_8_gblup_prediction_all_1_1000.rds") +T14_8_gblup_prediction_all_1001_2000=readRDS(file="T14_8_gblup_prediction_all_1001_2000.rds") +T14_8_gblup_prediction_all_2001_3000=readRDS(file="T14_8_gblup_prediction_all_2001_3000.rds") +T14_8_gblup_prediction_all_3001_4000=readRDS(file="T14_8_gblup_prediction_all_3001_4000.rds") +T14_8_gblup_prediction_all_4001_5000=readRDS(file="T14_8_gblup_prediction_all_4001_5000.rds") +T14_8_gblup_prediction_all_5001_6000=readRDS(file="T14_8_gblup_prediction_all_5001_6000.rds") +T14_8_gblup_prediction_all_6001_7297=readRDS(file="T14_8_gblup_prediction_all_6001_7297.rds") +T14_8_gblup_prediction_all=c(T14_8_gblup_prediction_all_1_1000,T14_8_gblup_prediction_all_1001_2000,T14_8_gblup_prediction_all_2001_3000,T14_8_gblup_prediction_all_3001_4000,T14_8_gblup_prediction_all_4001_5000,T14_8_gblup_prediction_all_5001_6000,T14_8_gblup_prediction_all_6001_7297) + +T14_8_gblup_variances_all_1_1000=readRDS(file="T14_8_gblup_variances_all_1_1000.rds") +T14_8_gblup_variances_all_1001_2000=readRDS(file="T14_8_gblup_variances_all_1001_2000.rds") +T14_8_gblup_variances_all_2001_3000=readRDS(file="T14_8_gblup_variances_all_2001_3000.rds") +T14_8_gblup_variances_all_3001_4000=readRDS(file="T14_8_gblup_variances_all_3001_4000.rds") +T14_8_gblup_variances_all_4001_5000=readRDS(file="T14_8_gblup_variances_all_4001_5000.rds") +T14_8_gblup_variances_all_5001_6000=readRDS(file="T14_8_gblup_variances_all_5001_6000.rds") +T14_8_gblup_variances_all_6001_7297=readRDS(file="T14_8_gblup_variances_all_6001_7297.rds") +T14_8_gblup_variances_all=c(T14_8_gblup_variances_all_1_1000,T14_8_gblup_variances_all_1001_2000,T14_8_gblup_variances_all_2001_3000,T14_8_gblup_variances_all_3001_4000,T14_8_gblup_variances_all_4001_5000,T14_8_gblup_variances_all_5001_6000,T14_8_gblup_variances_all_6001_7297) + +saveRDS(T14_8_gblup_prediction_all,"T14_8_gblup_prediction_all.rds") +saveRDS(T14_8_gblup_variances_all,"T14_8_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T14_8_gfblup_prediction_all_1_1000=readRDS(file="T14_8_gfblup_prediction_all_1_1000.rds") +T14_8_gfblup_prediction_all_1001_2000=readRDS(file="T14_8_gfblup_prediction_all_1001_2000.rds") +T14_8_gfblup_prediction_all_2001_3000=readRDS(file="T14_8_gfblup_prediction_all_2001_3000.rds") +T14_8_gfblup_prediction_all_3001_4000=readRDS(file="T14_8_gfblup_prediction_all_3001_4000.rds") +T14_8_gfblup_prediction_all_4001_5000=readRDS(file="T14_8_gfblup_prediction_all_4001_5000.rds") +T14_8_gfblup_prediction_all_5001_6000=readRDS(file="T14_8_gfblup_prediction_all_5001_6000.rds") +T14_8_gfblup_prediction_all_6001_7297=readRDS(file="T14_8_gfblup_prediction_all_6001_7297.rds") + +T14_8_gfblup_variances_all_1_1000=readRDS(file="T14_8_gfblup_variances_all_1_1000.rds") +T14_8_gfblup_variances_all_1001_2000=readRDS(file="T14_8_gfblup_variances_all_1001_2000.rds") +T14_8_gfblup_variances_all_2001_3000=readRDS(file="T14_8_gfblup_variances_all_2001_3000.rds") +T14_8_gfblup_variances_all_3001_4000=readRDS(file="T14_8_gfblup_variances_all_3001_4000.rds") +T14_8_gfblup_variances_all_4001_5000=readRDS(file="T14_8_gfblup_variances_all_4001_5000.rds") +T14_8_gfblup_variances_all_5001_6000=readRDS(file="T14_8_gfblup_variances_all_5001_6000.rds") +T14_8_gfblup_variances_all_6001_7297=readRDS(file="T14_8_gfblup_variances_all_6001_7297.rds") + +cycles=length(T14_8_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T14_8_gfblup_variances_all=rep(list(list()),cycles) +T14_8_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_1_1000[[r]]) + T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_1001_2000[[r]]) + T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_2001_3000[[r]]) + T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_3001_4000[[r]]) + T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_4001_5000[[r]]) + T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_5001_6000[[r]]) + T14_8_gfblup_prediction_all[[r]]<-c(T14_8_gfblup_prediction_all[[r]],T14_8_gfblup_prediction_all_6001_7297[[r]]) + + T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_1_1000[[r]]) + T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_1001_2000[[r]]) + T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_2001_3000[[r]]) + T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_3001_4000[[r]]) + T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_4001_5000[[r]]) + T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_5001_6000[[r]]) + T14_8_gfblup_variances_all[[r]]<-c(T14_8_gfblup_variances_all[[r]],T14_8_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T14_8_gfblup_prediction_all,"T14_8_gfblup_prediction_all.rds") +saveRDS(T14_8_gfblup_variances_all,"T14_8_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_1_gblup_prediction_all_1_1000=readRDS(file="T15_1_gblup_prediction_all_1_1000.rds") +T15_1_gblup_prediction_all_1001_2000=readRDS(file="T15_1_gblup_prediction_all_1001_2000.rds") +T15_1_gblup_prediction_all_2001_3000=readRDS(file="T15_1_gblup_prediction_all_2001_3000.rds") +T15_1_gblup_prediction_all_3001_4000=readRDS(file="T15_1_gblup_prediction_all_3001_4000.rds") +T15_1_gblup_prediction_all_4001_5000=readRDS(file="T15_1_gblup_prediction_all_4001_5000.rds") +T15_1_gblup_prediction_all_5001_6000=readRDS(file="T15_1_gblup_prediction_all_5001_6000.rds") +T15_1_gblup_prediction_all_6001_7297=readRDS(file="T15_1_gblup_prediction_all_6001_7297.rds") +T15_1_gblup_prediction_all=c(T15_1_gblup_prediction_all_1_1000,T15_1_gblup_prediction_all_1001_2000,T15_1_gblup_prediction_all_2001_3000,T15_1_gblup_prediction_all_3001_4000,T15_1_gblup_prediction_all_4001_5000,T15_1_gblup_prediction_all_5001_6000,T15_1_gblup_prediction_all_6001_7297) + +T15_1_gblup_variances_all_1_1000=readRDS(file="T15_1_gblup_variances_all_1_1000.rds") +T15_1_gblup_variances_all_1001_2000=readRDS(file="T15_1_gblup_variances_all_1001_2000.rds") +T15_1_gblup_variances_all_2001_3000=readRDS(file="T15_1_gblup_variances_all_2001_3000.rds") +T15_1_gblup_variances_all_3001_4000=readRDS(file="T15_1_gblup_variances_all_3001_4000.rds") +T15_1_gblup_variances_all_4001_5000=readRDS(file="T15_1_gblup_variances_all_4001_5000.rds") +T15_1_gblup_variances_all_5001_6000=readRDS(file="T15_1_gblup_variances_all_5001_6000.rds") +T15_1_gblup_variances_all_6001_7297=readRDS(file="T15_1_gblup_variances_all_6001_7297.rds") +T15_1_gblup_variances_all=c(T15_1_gblup_variances_all_1_1000,T15_1_gblup_variances_all_1001_2000,T15_1_gblup_variances_all_2001_3000,T15_1_gblup_variances_all_3001_4000,T15_1_gblup_variances_all_4001_5000,T15_1_gblup_variances_all_5001_6000,T15_1_gblup_variances_all_6001_7297) + +saveRDS(T15_1_gblup_prediction_all,"T15_1_gblup_prediction_all.rds") +saveRDS(T15_1_gblup_variances_all,"T15_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_1_gfblup_prediction_all_1_1000=readRDS(file="T15_1_gfblup_prediction_all_1_1000.rds") +T15_1_gfblup_prediction_all_1001_2000=readRDS(file="T15_1_gfblup_prediction_all_1001_2000.rds") +T15_1_gfblup_prediction_all_2001_3000=readRDS(file="T15_1_gfblup_prediction_all_2001_3000.rds") +T15_1_gfblup_prediction_all_3001_4000=readRDS(file="T15_1_gfblup_prediction_all_3001_4000.rds") +T15_1_gfblup_prediction_all_4001_5000=readRDS(file="T15_1_gfblup_prediction_all_4001_5000.rds") +T15_1_gfblup_prediction_all_5001_6000=readRDS(file="T15_1_gfblup_prediction_all_5001_6000.rds") +T15_1_gfblup_prediction_all_6001_7297=readRDS(file="T15_1_gfblup_prediction_all_6001_7297.rds") + +T15_1_gfblup_variances_all_1_1000=readRDS(file="T15_1_gfblup_variances_all_1_1000.rds") +T15_1_gfblup_variances_all_1001_2000=readRDS(file="T15_1_gfblup_variances_all_1001_2000.rds") +T15_1_gfblup_variances_all_2001_3000=readRDS(file="T15_1_gfblup_variances_all_2001_3000.rds") +T15_1_gfblup_variances_all_3001_4000=readRDS(file="T15_1_gfblup_variances_all_3001_4000.rds") +T15_1_gfblup_variances_all_4001_5000=readRDS(file="T15_1_gfblup_variances_all_4001_5000.rds") +T15_1_gfblup_variances_all_5001_6000=readRDS(file="T15_1_gfblup_variances_all_5001_6000.rds") +T15_1_gfblup_variances_all_6001_7297=readRDS(file="T15_1_gfblup_variances_all_6001_7297.rds") + +cycles=length(T15_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T15_1_gfblup_variances_all=rep(list(list()),cycles) +T15_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_1_1000[[r]]) + T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_1001_2000[[r]]) + T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_2001_3000[[r]]) + T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_3001_4000[[r]]) + T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_4001_5000[[r]]) + T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_5001_6000[[r]]) + T15_1_gfblup_prediction_all[[r]]<-c(T15_1_gfblup_prediction_all[[r]],T15_1_gfblup_prediction_all_6001_7297[[r]]) + + T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_1_1000[[r]]) + T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_1001_2000[[r]]) + T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_2001_3000[[r]]) + T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_3001_4000[[r]]) + T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_4001_5000[[r]]) + T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_5001_6000[[r]]) + T15_1_gfblup_variances_all[[r]]<-c(T15_1_gfblup_variances_all[[r]],T15_1_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T15_1_gfblup_prediction_all,"T15_1_gfblup_prediction_all.rds") +saveRDS(T15_1_gfblup_variances_all,"T15_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_2_gblup_prediction_all_1_1000=readRDS(file="T15_2_gblup_prediction_all_1_1000.rds") +T15_2_gblup_prediction_all_1001_2000=readRDS(file="T15_2_gblup_prediction_all_1001_2000.rds") +T15_2_gblup_prediction_all_2001_3000=readRDS(file="T15_2_gblup_prediction_all_2001_3000.rds") +T15_2_gblup_prediction_all_3001_4000=readRDS(file="T15_2_gblup_prediction_all_3001_4000.rds") +T15_2_gblup_prediction_all_4001_5000=readRDS(file="T15_2_gblup_prediction_all_4001_5000.rds") +T15_2_gblup_prediction_all_5001_6000=readRDS(file="T15_2_gblup_prediction_all_5001_6000.rds") +T15_2_gblup_prediction_all_6001_7297=readRDS(file="T15_2_gblup_prediction_all_6001_7297.rds") +T15_2_gblup_prediction_all=c(T15_2_gblup_prediction_all_1_1000,T15_2_gblup_prediction_all_1001_2000,T15_2_gblup_prediction_all_2001_3000,T15_2_gblup_prediction_all_3001_4000,T15_2_gblup_prediction_all_4001_5000,T15_2_gblup_prediction_all_5001_6000,T15_2_gblup_prediction_all_6001_7297) + +T15_2_gblup_variances_all_1_1000=readRDS(file="T15_2_gblup_variances_all_1_1000.rds") +T15_2_gblup_variances_all_1001_2000=readRDS(file="T15_2_gblup_variances_all_1001_2000.rds") +T15_2_gblup_variances_all_2001_3000=readRDS(file="T15_2_gblup_variances_all_2001_3000.rds") +T15_2_gblup_variances_all_3001_4000=readRDS(file="T15_2_gblup_variances_all_3001_4000.rds") +T15_2_gblup_variances_all_4001_5000=readRDS(file="T15_2_gblup_variances_all_4001_5000.rds") +T15_2_gblup_variances_all_5001_6000=readRDS(file="T15_2_gblup_variances_all_5001_6000.rds") +T15_2_gblup_variances_all_6001_7297=readRDS(file="T15_2_gblup_variances_all_6001_7297.rds") +T15_2_gblup_variances_all=c(T15_2_gblup_variances_all_1_1000,T15_2_gblup_variances_all_1001_2000,T15_2_gblup_variances_all_2001_3000,T15_2_gblup_variances_all_3001_4000,T15_2_gblup_variances_all_4001_5000,T15_2_gblup_variances_all_5001_6000,T15_2_gblup_variances_all_6001_7297) + +saveRDS(T15_2_gblup_prediction_all,"T15_2_gblup_prediction_all.rds") +saveRDS(T15_2_gblup_variances_all,"T15_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_2_gfblup_prediction_all_1_1000=readRDS(file="T15_2_gfblup_prediction_all_1_1000.rds") +T15_2_gfblup_prediction_all_1001_2000=readRDS(file="T15_2_gfblup_prediction_all_1001_2000.rds") +T15_2_gfblup_prediction_all_2001_3000=readRDS(file="T15_2_gfblup_prediction_all_2001_3000.rds") +T15_2_gfblup_prediction_all_3001_4000=readRDS(file="T15_2_gfblup_prediction_all_3001_4000.rds") +T15_2_gfblup_prediction_all_4001_5000=readRDS(file="T15_2_gfblup_prediction_all_4001_5000.rds") +T15_2_gfblup_prediction_all_5001_6000=readRDS(file="T15_2_gfblup_prediction_all_5001_6000.rds") +T15_2_gfblup_prediction_all_6001_7297=readRDS(file="T15_2_gfblup_prediction_all_6001_7297.rds") + +T15_2_gfblup_variances_all_1_1000=readRDS(file="T15_2_gfblup_variances_all_1_1000.rds") +T15_2_gfblup_variances_all_1001_2000=readRDS(file="T15_2_gfblup_variances_all_1001_2000.rds") +T15_2_gfblup_variances_all_2001_3000=readRDS(file="T15_2_gfblup_variances_all_2001_3000.rds") +T15_2_gfblup_variances_all_3001_4000=readRDS(file="T15_2_gfblup_variances_all_3001_4000.rds") +T15_2_gfblup_variances_all_4001_5000=readRDS(file="T15_2_gfblup_variances_all_4001_5000.rds") +T15_2_gfblup_variances_all_5001_6000=readRDS(file="T15_2_gfblup_variances_all_5001_6000.rds") +T15_2_gfblup_variances_all_6001_7297=readRDS(file="T15_2_gfblup_variances_all_6001_7297.rds") + +cycles=length(T15_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T15_2_gfblup_variances_all=rep(list(list()),cycles) +T15_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_1_1000[[r]]) + T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_1001_2000[[r]]) + T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_2001_3000[[r]]) + T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_3001_4000[[r]]) + T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_4001_5000[[r]]) + T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_5001_6000[[r]]) + T15_2_gfblup_prediction_all[[r]]<-c(T15_2_gfblup_prediction_all[[r]],T15_2_gfblup_prediction_all_6001_7297[[r]]) + + T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_1_1000[[r]]) + T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_1001_2000[[r]]) + T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_2001_3000[[r]]) + T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_3001_4000[[r]]) + T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_4001_5000[[r]]) + T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_5001_6000[[r]]) + T15_2_gfblup_variances_all[[r]]<-c(T15_2_gfblup_variances_all[[r]],T15_2_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T15_2_gfblup_prediction_all,"T15_2_gfblup_prediction_all.rds") +saveRDS(T15_2_gfblup_variances_all,"T15_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_3_gblup_prediction_all_1_1000=readRDS(file="T15_3_gblup_prediction_all_1_1000.rds") +T15_3_gblup_prediction_all_1001_2000=readRDS(file="T15_3_gblup_prediction_all_1001_2000.rds") +T15_3_gblup_prediction_all_2001_3000=readRDS(file="T15_3_gblup_prediction_all_2001_3000.rds") +T15_3_gblup_prediction_all_3001_4000=readRDS(file="T15_3_gblup_prediction_all_3001_4000.rds") +T15_3_gblup_prediction_all_4001_5000=readRDS(file="T15_3_gblup_prediction_all_4001_5000.rds") +T15_3_gblup_prediction_all_5001_6000=readRDS(file="T15_3_gblup_prediction_all_5001_6000.rds") +T15_3_gblup_prediction_all_6001_7297=readRDS(file="T15_3_gblup_prediction_all_6001_7297.rds") +T15_3_gblup_prediction_all=c(T15_3_gblup_prediction_all_1_1000,T15_3_gblup_prediction_all_1001_2000,T15_3_gblup_prediction_all_2001_3000,T15_3_gblup_prediction_all_3001_4000,T15_3_gblup_prediction_all_4001_5000,T15_3_gblup_prediction_all_5001_6000,T15_3_gblup_prediction_all_6001_7297) + +T15_3_gblup_variances_all_1_1000=readRDS(file="T15_3_gblup_variances_all_1_1000.rds") +T15_3_gblup_variances_all_1001_2000=readRDS(file="T15_3_gblup_variances_all_1001_2000.rds") +T15_3_gblup_variances_all_2001_3000=readRDS(file="T15_3_gblup_variances_all_2001_3000.rds") +T15_3_gblup_variances_all_3001_4000=readRDS(file="T15_3_gblup_variances_all_3001_4000.rds") +T15_3_gblup_variances_all_4001_5000=readRDS(file="T15_3_gblup_variances_all_4001_5000.rds") +T15_3_gblup_variances_all_5001_6000=readRDS(file="T15_3_gblup_variances_all_5001_6000.rds") +T15_3_gblup_variances_all_6001_7297=readRDS(file="T15_3_gblup_variances_all_6001_7297.rds") +T15_3_gblup_variances_all=c(T15_3_gblup_variances_all_1_1000,T15_3_gblup_variances_all_1001_2000,T15_3_gblup_variances_all_2001_3000,T15_3_gblup_variances_all_3001_4000,T15_3_gblup_variances_all_4001_5000,T15_3_gblup_variances_all_5001_6000,T15_3_gblup_variances_all_6001_7297) + +saveRDS(T15_3_gblup_prediction_all,"T15_3_gblup_prediction_all.rds") +saveRDS(T15_3_gblup_variances_all,"T15_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_3_gfblup_prediction_all_1_1000=readRDS(file="T15_3_gfblup_prediction_all_1_1000.rds") +T15_3_gfblup_prediction_all_1001_2000=readRDS(file="T15_3_gfblup_prediction_all_1001_2000.rds") +T15_3_gfblup_prediction_all_2001_3000=readRDS(file="T15_3_gfblup_prediction_all_2001_3000.rds") +T15_3_gfblup_prediction_all_3001_4000=readRDS(file="T15_3_gfblup_prediction_all_3001_4000.rds") +T15_3_gfblup_prediction_all_4001_5000=readRDS(file="T15_3_gfblup_prediction_all_4001_5000.rds") +T15_3_gfblup_prediction_all_5001_6000=readRDS(file="T15_3_gfblup_prediction_all_5001_6000.rds") +T15_3_gfblup_prediction_all_6001_7297=readRDS(file="T15_3_gfblup_prediction_all_6001_7297.rds") + +T15_3_gfblup_variances_all_1_1000=readRDS(file="T15_3_gfblup_variances_all_1_1000.rds") +T15_3_gfblup_variances_all_1001_2000=readRDS(file="T15_3_gfblup_variances_all_1001_2000.rds") +T15_3_gfblup_variances_all_2001_3000=readRDS(file="T15_3_gfblup_variances_all_2001_3000.rds") +T15_3_gfblup_variances_all_3001_4000=readRDS(file="T15_3_gfblup_variances_all_3001_4000.rds") +T15_3_gfblup_variances_all_4001_5000=readRDS(file="T15_3_gfblup_variances_all_4001_5000.rds") +T15_3_gfblup_variances_all_5001_6000=readRDS(file="T15_3_gfblup_variances_all_5001_6000.rds") +T15_3_gfblup_variances_all_6001_7297=readRDS(file="T15_3_gfblup_variances_all_6001_7297.rds") + +cycles=length(T15_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T15_3_gfblup_variances_all=rep(list(list()),cycles) +T15_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_1_1000[[r]]) + T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_1001_2000[[r]]) + T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_2001_3000[[r]]) + T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_3001_4000[[r]]) + T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_4001_5000[[r]]) + T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_5001_6000[[r]]) + T15_3_gfblup_prediction_all[[r]]<-c(T15_3_gfblup_prediction_all[[r]],T15_3_gfblup_prediction_all_6001_7297[[r]]) + + T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_1_1000[[r]]) + T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_1001_2000[[r]]) + T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_2001_3000[[r]]) + T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_3001_4000[[r]]) + T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_4001_5000[[r]]) + T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_5001_6000[[r]]) + T15_3_gfblup_variances_all[[r]]<-c(T15_3_gfblup_variances_all[[r]],T15_3_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T15_3_gfblup_prediction_all,"T15_3_gfblup_prediction_all.rds") +saveRDS(T15_3_gfblup_variances_all,"T15_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_4_gblup_prediction_all_1_1000=readRDS(file="T15_4_gblup_prediction_all_1_1000.rds") +T15_4_gblup_prediction_all_1001_2000=readRDS(file="T15_4_gblup_prediction_all_1001_2000.rds") +T15_4_gblup_prediction_all_2001_3000=readRDS(file="T15_4_gblup_prediction_all_2001_3000.rds") +T15_4_gblup_prediction_all_3001_4000=readRDS(file="T15_4_gblup_prediction_all_3001_4000.rds") +T15_4_gblup_prediction_all_4001_5000=readRDS(file="T15_4_gblup_prediction_all_4001_5000.rds") +T15_4_gblup_prediction_all_5001_6000=readRDS(file="T15_4_gblup_prediction_all_5001_6000.rds") +T15_4_gblup_prediction_all_6001_7297=readRDS(file="T15_4_gblup_prediction_all_6001_7297.rds") +T15_4_gblup_prediction_all=c(T15_4_gblup_prediction_all_1_1000,T15_4_gblup_prediction_all_1001_2000,T15_4_gblup_prediction_all_2001_3000,T15_4_gblup_prediction_all_3001_4000,T15_4_gblup_prediction_all_4001_5000,T15_4_gblup_prediction_all_5001_6000,T15_4_gblup_prediction_all_6001_7297) + +T15_4_gblup_variances_all_1_1000=readRDS(file="T15_4_gblup_variances_all_1_1000.rds") +T15_4_gblup_variances_all_1001_2000=readRDS(file="T15_4_gblup_variances_all_1001_2000.rds") +T15_4_gblup_variances_all_2001_3000=readRDS(file="T15_4_gblup_variances_all_2001_3000.rds") +T15_4_gblup_variances_all_3001_4000=readRDS(file="T15_4_gblup_variances_all_3001_4000.rds") +T15_4_gblup_variances_all_4001_5000=readRDS(file="T15_4_gblup_variances_all_4001_5000.rds") +T15_4_gblup_variances_all_5001_6000=readRDS(file="T15_4_gblup_variances_all_5001_6000.rds") +T15_4_gblup_variances_all_6001_7297=readRDS(file="T15_4_gblup_variances_all_6001_7297.rds") +T15_4_gblup_variances_all=c(T15_4_gblup_variances_all_1_1000,T15_4_gblup_variances_all_1001_2000,T15_4_gblup_variances_all_2001_3000,T15_4_gblup_variances_all_3001_4000,T15_4_gblup_variances_all_4001_5000,T15_4_gblup_variances_all_5001_6000,T15_4_gblup_variances_all_6001_7297) + +saveRDS(T15_4_gblup_prediction_all,"T15_4_gblup_prediction_all.rds") +saveRDS(T15_4_gblup_variances_all,"T15_4_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_4_gfblup_prediction_all_1_1000=readRDS(file="T15_4_gfblup_prediction_all_1_1000.rds") +T15_4_gfblup_prediction_all_1001_2000=readRDS(file="T15_4_gfblup_prediction_all_1001_2000.rds") +T15_4_gfblup_prediction_all_2001_3000=readRDS(file="T15_4_gfblup_prediction_all_2001_3000.rds") +T15_4_gfblup_prediction_all_3001_4000=readRDS(file="T15_4_gfblup_prediction_all_3001_4000.rds") +T15_4_gfblup_prediction_all_4001_5000=readRDS(file="T15_4_gfblup_prediction_all_4001_5000.rds") +T15_4_gfblup_prediction_all_5001_6000=readRDS(file="T15_4_gfblup_prediction_all_5001_6000.rds") +T15_4_gfblup_prediction_all_6001_7297=readRDS(file="T15_4_gfblup_prediction_all_6001_7297.rds") + +T15_4_gfblup_variances_all_1_1000=readRDS(file="T15_4_gfblup_variances_all_1_1000.rds") +T15_4_gfblup_variances_all_1001_2000=readRDS(file="T15_4_gfblup_variances_all_1001_2000.rds") +T15_4_gfblup_variances_all_2001_3000=readRDS(file="T15_4_gfblup_variances_all_2001_3000.rds") +T15_4_gfblup_variances_all_3001_4000=readRDS(file="T15_4_gfblup_variances_all_3001_4000.rds") +T15_4_gfblup_variances_all_4001_5000=readRDS(file="T15_4_gfblup_variances_all_4001_5000.rds") +T15_4_gfblup_variances_all_5001_6000=readRDS(file="T15_4_gfblup_variances_all_5001_6000.rds") +T15_4_gfblup_variances_all_6001_7297=readRDS(file="T15_4_gfblup_variances_all_6001_7297.rds") + +cycles=length(T15_4_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T15_4_gfblup_variances_all=rep(list(list()),cycles) +T15_4_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_1_1000[[r]]) + T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_1001_2000[[r]]) + T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_2001_3000[[r]]) + T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_3001_4000[[r]]) + T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_4001_5000[[r]]) + T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_5001_6000[[r]]) + T15_4_gfblup_prediction_all[[r]]<-c(T15_4_gfblup_prediction_all[[r]],T15_4_gfblup_prediction_all_6001_7297[[r]]) + + T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_1_1000[[r]]) + T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_1001_2000[[r]]) + T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_2001_3000[[r]]) + T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_3001_4000[[r]]) + T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_4001_5000[[r]]) + T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_5001_6000[[r]]) + T15_4_gfblup_variances_all[[r]]<-c(T15_4_gfblup_variances_all[[r]],T15_4_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T15_4_gfblup_prediction_all,"T15_4_gfblup_prediction_all.rds") +saveRDS(T15_4_gfblup_variances_all,"T15_4_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_5_gblup_prediction_all_1_1000=readRDS(file="T15_5_gblup_prediction_all_1_1000.rds") +T15_5_gblup_prediction_all_1001_2000=readRDS(file="T15_5_gblup_prediction_all_1001_2000.rds") +T15_5_gblup_prediction_all_2001_3000=readRDS(file="T15_5_gblup_prediction_all_2001_3000.rds") +T15_5_gblup_prediction_all_3001_4000=readRDS(file="T15_5_gblup_prediction_all_3001_4000.rds") +T15_5_gblup_prediction_all_4001_5000=readRDS(file="T15_5_gblup_prediction_all_4001_5000.rds") +T15_5_gblup_prediction_all_5001_6000=readRDS(file="T15_5_gblup_prediction_all_5001_6000.rds") +T15_5_gblup_prediction_all_6001_7297=readRDS(file="T15_5_gblup_prediction_all_6001_7297.rds") +T15_5_gblup_prediction_all=c(T15_5_gblup_prediction_all_1_1000,T15_5_gblup_prediction_all_1001_2000,T15_5_gblup_prediction_all_2001_3000,T15_5_gblup_prediction_all_3001_4000,T15_5_gblup_prediction_all_4001_5000,T15_5_gblup_prediction_all_5001_6000,T15_5_gblup_prediction_all_6001_7297) + +T15_5_gblup_variances_all_1_1000=readRDS(file="T15_5_gblup_variances_all_1_1000.rds") +T15_5_gblup_variances_all_1001_2000=readRDS(file="T15_5_gblup_variances_all_1001_2000.rds") +T15_5_gblup_variances_all_2001_3000=readRDS(file="T15_5_gblup_variances_all_2001_3000.rds") +T15_5_gblup_variances_all_3001_4000=readRDS(file="T15_5_gblup_variances_all_3001_4000.rds") +T15_5_gblup_variances_all_4001_5000=readRDS(file="T15_5_gblup_variances_all_4001_5000.rds") +T15_5_gblup_variances_all_5001_6000=readRDS(file="T15_5_gblup_variances_all_5001_6000.rds") +T15_5_gblup_variances_all_6001_7297=readRDS(file="T15_5_gblup_variances_all_6001_7297.rds") +T15_5_gblup_variances_all=c(T15_5_gblup_variances_all_1_1000,T15_5_gblup_variances_all_1001_2000,T15_5_gblup_variances_all_2001_3000,T15_5_gblup_variances_all_3001_4000,T15_5_gblup_variances_all_4001_5000,T15_5_gblup_variances_all_5001_6000,T15_5_gblup_variances_all_6001_7297) + +saveRDS(T15_5_gblup_prediction_all,"T15_5_gblup_prediction_all.rds") +saveRDS(T15_5_gblup_variances_all,"T15_5_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_5_gfblup_prediction_all_1_1000=readRDS(file="T15_5_gfblup_prediction_all_1_1000.rds") +T15_5_gfblup_prediction_all_1001_2000=readRDS(file="T15_5_gfblup_prediction_all_1001_2000.rds") +T15_5_gfblup_prediction_all_2001_3000=readRDS(file="T15_5_gfblup_prediction_all_2001_3000.rds") +T15_5_gfblup_prediction_all_3001_4000=readRDS(file="T15_5_gfblup_prediction_all_3001_4000.rds") +T15_5_gfblup_prediction_all_4001_5000=readRDS(file="T15_5_gfblup_prediction_all_4001_5000.rds") +T15_5_gfblup_prediction_all_5001_6000=readRDS(file="T15_5_gfblup_prediction_all_5001_6000.rds") +T15_5_gfblup_prediction_all_6001_7297=readRDS(file="T15_5_gfblup_prediction_all_6001_7297.rds") + +T15_5_gfblup_variances_all_1_1000=readRDS(file="T15_5_gfblup_variances_all_1_1000.rds") +T15_5_gfblup_variances_all_1001_2000=readRDS(file="T15_5_gfblup_variances_all_1001_2000.rds") +T15_5_gfblup_variances_all_2001_3000=readRDS(file="T15_5_gfblup_variances_all_2001_3000.rds") +T15_5_gfblup_variances_all_3001_4000=readRDS(file="T15_5_gfblup_variances_all_3001_4000.rds") +T15_5_gfblup_variances_all_4001_5000=readRDS(file="T15_5_gfblup_variances_all_4001_5000.rds") +T15_5_gfblup_variances_all_5001_6000=readRDS(file="T15_5_gfblup_variances_all_5001_6000.rds") +T15_5_gfblup_variances_all_6001_7297=readRDS(file="T15_5_gfblup_variances_all_6001_7297.rds") + +cycles=length(T15_5_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T15_5_gfblup_variances_all=rep(list(list()),cycles) +T15_5_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_1_1000[[r]]) + T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_1001_2000[[r]]) + T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_2001_3000[[r]]) + T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_3001_4000[[r]]) + T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_4001_5000[[r]]) + T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_5001_6000[[r]]) + T15_5_gfblup_prediction_all[[r]]<-c(T15_5_gfblup_prediction_all[[r]],T15_5_gfblup_prediction_all_6001_7297[[r]]) + + T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_1_1000[[r]]) + T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_1001_2000[[r]]) + T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_2001_3000[[r]]) + T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_3001_4000[[r]]) + T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_4001_5000[[r]]) + T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_5001_6000[[r]]) + T15_5_gfblup_variances_all[[r]]<-c(T15_5_gfblup_variances_all[[r]],T15_5_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T15_5_gfblup_prediction_all,"T15_5_gfblup_prediction_all.rds") +saveRDS(T15_5_gfblup_variances_all,"T15_5_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_6_gblup_prediction_all_1_1000=readRDS(file="T15_6_gblup_prediction_all_1_1000.rds") +T15_6_gblup_prediction_all_1001_2000=readRDS(file="T15_6_gblup_prediction_all_1001_2000.rds") +T15_6_gblup_prediction_all_2001_3000=readRDS(file="T15_6_gblup_prediction_all_2001_3000.rds") +T15_6_gblup_prediction_all_3001_4000=readRDS(file="T15_6_gblup_prediction_all_3001_4000.rds") +T15_6_gblup_prediction_all_4001_5000=readRDS(file="T15_6_gblup_prediction_all_4001_5000.rds") +T15_6_gblup_prediction_all_5001_6000=readRDS(file="T15_6_gblup_prediction_all_5001_6000.rds") +T15_6_gblup_prediction_all_6001_7297=readRDS(file="T15_6_gblup_prediction_all_6001_7297.rds") +T15_6_gblup_prediction_all=c(T15_6_gblup_prediction_all_1_1000,T15_6_gblup_prediction_all_1001_2000,T15_6_gblup_prediction_all_2001_3000,T15_6_gblup_prediction_all_3001_4000,T15_6_gblup_prediction_all_4001_5000,T15_6_gblup_prediction_all_5001_6000,T15_6_gblup_prediction_all_6001_7297) + +T15_6_gblup_variances_all_1_1000=readRDS(file="T15_6_gblup_variances_all_1_1000.rds") +T15_6_gblup_variances_all_1001_2000=readRDS(file="T15_6_gblup_variances_all_1001_2000.rds") +T15_6_gblup_variances_all_2001_3000=readRDS(file="T15_6_gblup_variances_all_2001_3000.rds") +T15_6_gblup_variances_all_3001_4000=readRDS(file="T15_6_gblup_variances_all_3001_4000.rds") +T15_6_gblup_variances_all_4001_5000=readRDS(file="T15_6_gblup_variances_all_4001_5000.rds") +T15_6_gblup_variances_all_5001_6000=readRDS(file="T15_6_gblup_variances_all_5001_6000.rds") +T15_6_gblup_variances_all_6001_7297=readRDS(file="T15_6_gblup_variances_all_6001_7297.rds") +T15_6_gblup_variances_all=c(T15_6_gblup_variances_all_1_1000,T15_6_gblup_variances_all_1001_2000,T15_6_gblup_variances_all_2001_3000,T15_6_gblup_variances_all_3001_4000,T15_6_gblup_variances_all_4001_5000,T15_6_gblup_variances_all_5001_6000,T15_6_gblup_variances_all_6001_7297) + +saveRDS(T15_6_gblup_prediction_all,"T15_6_gblup_prediction_all.rds") +saveRDS(T15_6_gblup_variances_all,"T15_6_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_6_gfblup_prediction_all_1_1000=readRDS(file="T15_6_gfblup_prediction_all_1_1000.rds") +T15_6_gfblup_prediction_all_1001_2000=readRDS(file="T15_6_gfblup_prediction_all_1001_2000.rds") +T15_6_gfblup_prediction_all_2001_3000=readRDS(file="T15_6_gfblup_prediction_all_2001_3000.rds") +T15_6_gfblup_prediction_all_3001_4000=readRDS(file="T15_6_gfblup_prediction_all_3001_4000.rds") +T15_6_gfblup_prediction_all_4001_5000=readRDS(file="T15_6_gfblup_prediction_all_4001_5000.rds") +T15_6_gfblup_prediction_all_5001_6000=readRDS(file="T15_6_gfblup_prediction_all_5001_6000.rds") +T15_6_gfblup_prediction_all_6001_7297=readRDS(file="T15_6_gfblup_prediction_all_6001_7297.rds") + +T15_6_gfblup_variances_all_1_1000=readRDS(file="T15_6_gfblup_variances_all_1_1000.rds") +T15_6_gfblup_variances_all_1001_2000=readRDS(file="T15_6_gfblup_variances_all_1001_2000.rds") +T15_6_gfblup_variances_all_2001_3000=readRDS(file="T15_6_gfblup_variances_all_2001_3000.rds") +T15_6_gfblup_variances_all_3001_4000=readRDS(file="T15_6_gfblup_variances_all_3001_4000.rds") +T15_6_gfblup_variances_all_4001_5000=readRDS(file="T15_6_gfblup_variances_all_4001_5000.rds") +T15_6_gfblup_variances_all_5001_6000=readRDS(file="T15_6_gfblup_variances_all_5001_6000.rds") +T15_6_gfblup_variances_all_6001_7297=readRDS(file="T15_6_gfblup_variances_all_6001_7297.rds") + +cycles=length(T15_6_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T15_6_gfblup_variances_all=rep(list(list()),cycles) +T15_6_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_1_1000[[r]]) + T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_1001_2000[[r]]) + T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_2001_3000[[r]]) + T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_3001_4000[[r]]) + T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_4001_5000[[r]]) + T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_5001_6000[[r]]) + T15_6_gfblup_prediction_all[[r]]<-c(T15_6_gfblup_prediction_all[[r]],T15_6_gfblup_prediction_all_6001_7297[[r]]) + + T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_1_1000[[r]]) + T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_1001_2000[[r]]) + T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_2001_3000[[r]]) + T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_3001_4000[[r]]) + T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_4001_5000[[r]]) + T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_5001_6000[[r]]) + T15_6_gfblup_variances_all[[r]]<-c(T15_6_gfblup_variances_all[[r]],T15_6_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T15_6_gfblup_prediction_all,"T15_6_gfblup_prediction_all.rds") +saveRDS(T15_6_gfblup_variances_all,"T15_6_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_7_gblup_prediction_all_1_1000=readRDS(file="T15_7_gblup_prediction_all_1_1000.rds") +T15_7_gblup_prediction_all_1001_2000=readRDS(file="T15_7_gblup_prediction_all_1001_2000.rds") +T15_7_gblup_prediction_all_2001_3000=readRDS(file="T15_7_gblup_prediction_all_2001_3000.rds") +T15_7_gblup_prediction_all_3001_4000=readRDS(file="T15_7_gblup_prediction_all_3001_4000.rds") +T15_7_gblup_prediction_all_4001_5000=readRDS(file="T15_7_gblup_prediction_all_4001_5000.rds") +T15_7_gblup_prediction_all_5001_6000=readRDS(file="T15_7_gblup_prediction_all_5001_6000.rds") +T15_7_gblup_prediction_all_6001_7297=readRDS(file="T15_7_gblup_prediction_all_6001_7297.rds") +T15_7_gblup_prediction_all=c(T15_7_gblup_prediction_all_1_1000,T15_7_gblup_prediction_all_1001_2000,T15_7_gblup_prediction_all_2001_3000,T15_7_gblup_prediction_all_3001_4000,T15_7_gblup_prediction_all_4001_5000,T15_7_gblup_prediction_all_5001_6000,T15_7_gblup_prediction_all_6001_7297) + +T15_7_gblup_variances_all_1_1000=readRDS(file="T15_7_gblup_variances_all_1_1000.rds") +T15_7_gblup_variances_all_1001_2000=readRDS(file="T15_7_gblup_variances_all_1001_2000.rds") +T15_7_gblup_variances_all_2001_3000=readRDS(file="T15_7_gblup_variances_all_2001_3000.rds") +T15_7_gblup_variances_all_3001_4000=readRDS(file="T15_7_gblup_variances_all_3001_4000.rds") +T15_7_gblup_variances_all_4001_5000=readRDS(file="T15_7_gblup_variances_all_4001_5000.rds") +T15_7_gblup_variances_all_5001_6000=readRDS(file="T15_7_gblup_variances_all_5001_6000.rds") +T15_7_gblup_variances_all_6001_7297=readRDS(file="T15_7_gblup_variances_all_6001_7297.rds") +T15_7_gblup_variances_all=c(T15_7_gblup_variances_all_1_1000,T15_7_gblup_variances_all_1001_2000,T15_7_gblup_variances_all_2001_3000,T15_7_gblup_variances_all_3001_4000,T15_7_gblup_variances_all_4001_5000,T15_7_gblup_variances_all_5001_6000,T15_7_gblup_variances_all_6001_7297) + +saveRDS(T15_7_gblup_prediction_all,"T15_7_gblup_prediction_all.rds") +saveRDS(T15_7_gblup_variances_all,"T15_7_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_7_gfblup_prediction_all_1_1000=readRDS(file="T15_7_gfblup_prediction_all_1_1000.rds") +T15_7_gfblup_prediction_all_1001_2000=readRDS(file="T15_7_gfblup_prediction_all_1001_2000.rds") +T15_7_gfblup_prediction_all_2001_3000=readRDS(file="T15_7_gfblup_prediction_all_2001_3000.rds") +T15_7_gfblup_prediction_all_3001_4000=readRDS(file="T15_7_gfblup_prediction_all_3001_4000.rds") +T15_7_gfblup_prediction_all_4001_5000=readRDS(file="T15_7_gfblup_prediction_all_4001_5000.rds") +T15_7_gfblup_prediction_all_5001_6000=readRDS(file="T15_7_gfblup_prediction_all_5001_6000.rds") +T15_7_gfblup_prediction_all_6001_7297=readRDS(file="T15_7_gfblup_prediction_all_6001_7297.rds") + +T15_7_gfblup_variances_all_1_1000=readRDS(file="T15_7_gfblup_variances_all_1_1000.rds") +T15_7_gfblup_variances_all_1001_2000=readRDS(file="T15_7_gfblup_variances_all_1001_2000.rds") +T15_7_gfblup_variances_all_2001_3000=readRDS(file="T15_7_gfblup_variances_all_2001_3000.rds") +T15_7_gfblup_variances_all_3001_4000=readRDS(file="T15_7_gfblup_variances_all_3001_4000.rds") +T15_7_gfblup_variances_all_4001_5000=readRDS(file="T15_7_gfblup_variances_all_4001_5000.rds") +T15_7_gfblup_variances_all_5001_6000=readRDS(file="T15_7_gfblup_variances_all_5001_6000.rds") +T15_7_gfblup_variances_all_6001_7297=readRDS(file="T15_7_gfblup_variances_all_6001_7297.rds") + +cycles=length(T15_7_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T15_7_gfblup_variances_all=rep(list(list()),cycles) +T15_7_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_1_1000[[r]]) + T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_1001_2000[[r]]) + T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_2001_3000[[r]]) + T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_3001_4000[[r]]) + T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_4001_5000[[r]]) + T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_5001_6000[[r]]) + T15_7_gfblup_prediction_all[[r]]<-c(T15_7_gfblup_prediction_all[[r]],T15_7_gfblup_prediction_all_6001_7297[[r]]) + + T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_1_1000[[r]]) + T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_1001_2000[[r]]) + T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_2001_3000[[r]]) + T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_3001_4000[[r]]) + T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_4001_5000[[r]]) + T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_5001_6000[[r]]) + T15_7_gfblup_variances_all[[r]]<-c(T15_7_gfblup_variances_all[[r]],T15_7_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T15_7_gfblup_prediction_all,"T15_7_gfblup_prediction_all.rds") +saveRDS(T15_7_gfblup_variances_all,"T15_7_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_8_gblup_prediction_all_1_1000=readRDS(file="T15_8_gblup_prediction_all_1_1000.rds") +T15_8_gblup_prediction_all_1001_2000=readRDS(file="T15_8_gblup_prediction_all_1001_2000.rds") +T15_8_gblup_prediction_all_2001_3000=readRDS(file="T15_8_gblup_prediction_all_2001_3000.rds") +T15_8_gblup_prediction_all_3001_4000=readRDS(file="T15_8_gblup_prediction_all_3001_4000.rds") +T15_8_gblup_prediction_all_4001_5000=readRDS(file="T15_8_gblup_prediction_all_4001_5000.rds") +T15_8_gblup_prediction_all_5001_6000=readRDS(file="T15_8_gblup_prediction_all_5001_6000.rds") +T15_8_gblup_prediction_all_6001_7297=readRDS(file="T15_8_gblup_prediction_all_6001_7297.rds") +T15_8_gblup_prediction_all=c(T15_8_gblup_prediction_all_1_1000,T15_8_gblup_prediction_all_1001_2000,T15_8_gblup_prediction_all_2001_3000,T15_8_gblup_prediction_all_3001_4000,T15_8_gblup_prediction_all_4001_5000,T15_8_gblup_prediction_all_5001_6000,T15_8_gblup_prediction_all_6001_7297) + +T15_8_gblup_variances_all_1_1000=readRDS(file="T15_8_gblup_variances_all_1_1000.rds") +T15_8_gblup_variances_all_1001_2000=readRDS(file="T15_8_gblup_variances_all_1001_2000.rds") +T15_8_gblup_variances_all_2001_3000=readRDS(file="T15_8_gblup_variances_all_2001_3000.rds") +T15_8_gblup_variances_all_3001_4000=readRDS(file="T15_8_gblup_variances_all_3001_4000.rds") +T15_8_gblup_variances_all_4001_5000=readRDS(file="T15_8_gblup_variances_all_4001_5000.rds") +T15_8_gblup_variances_all_5001_6000=readRDS(file="T15_8_gblup_variances_all_5001_6000.rds") +T15_8_gblup_variances_all_6001_7297=readRDS(file="T15_8_gblup_variances_all_6001_7297.rds") +T15_8_gblup_variances_all=c(T15_8_gblup_variances_all_1_1000,T15_8_gblup_variances_all_1001_2000,T15_8_gblup_variances_all_2001_3000,T15_8_gblup_variances_all_3001_4000,T15_8_gblup_variances_all_4001_5000,T15_8_gblup_variances_all_5001_6000,T15_8_gblup_variances_all_6001_7297) + +saveRDS(T15_8_gblup_prediction_all,"T15_8_gblup_prediction_all.rds") +saveRDS(T15_8_gblup_variances_all,"T15_8_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T15_8_gfblup_prediction_all_1_1000=readRDS(file="T15_8_gfblup_prediction_all_1_1000.rds") +T15_8_gfblup_prediction_all_1001_2000=readRDS(file="T15_8_gfblup_prediction_all_1001_2000.rds") +T15_8_gfblup_prediction_all_2001_3000=readRDS(file="T15_8_gfblup_prediction_all_2001_3000.rds") +T15_8_gfblup_prediction_all_3001_4000=readRDS(file="T15_8_gfblup_prediction_all_3001_4000.rds") +T15_8_gfblup_prediction_all_4001_5000=readRDS(file="T15_8_gfblup_prediction_all_4001_5000.rds") +T15_8_gfblup_prediction_all_5001_6000=readRDS(file="T15_8_gfblup_prediction_all_5001_6000.rds") +T15_8_gfblup_prediction_all_6001_7297=readRDS(file="T15_8_gfblup_prediction_all_6001_7297.rds") + +T15_8_gfblup_variances_all_1_1000=readRDS(file="T15_8_gfblup_variances_all_1_1000.rds") +T15_8_gfblup_variances_all_1001_2000=readRDS(file="T15_8_gfblup_variances_all_1001_2000.rds") +T15_8_gfblup_variances_all_2001_3000=readRDS(file="T15_8_gfblup_variances_all_2001_3000.rds") +T15_8_gfblup_variances_all_3001_4000=readRDS(file="T15_8_gfblup_variances_all_3001_4000.rds") +T15_8_gfblup_variances_all_4001_5000=readRDS(file="T15_8_gfblup_variances_all_4001_5000.rds") +T15_8_gfblup_variances_all_5001_6000=readRDS(file="T15_8_gfblup_variances_all_5001_6000.rds") +T15_8_gfblup_variances_all_6001_7297=readRDS(file="T15_8_gfblup_variances_all_6001_7297.rds") + +cycles=length(T15_8_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T15_8_gfblup_variances_all=rep(list(list()),cycles) +T15_8_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_1_1000[[r]]) + T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_1001_2000[[r]]) + T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_2001_3000[[r]]) + T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_3001_4000[[r]]) + T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_4001_5000[[r]]) + T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_5001_6000[[r]]) + T15_8_gfblup_prediction_all[[r]]<-c(T15_8_gfblup_prediction_all[[r]],T15_8_gfblup_prediction_all_6001_7297[[r]]) + + T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_1_1000[[r]]) + T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_1001_2000[[r]]) + T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_2001_3000[[r]]) + T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_3001_4000[[r]]) + T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_4001_5000[[r]]) + T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_5001_6000[[r]]) + T15_8_gfblup_variances_all[[r]]<-c(T15_8_gfblup_variances_all[[r]],T15_8_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T15_8_gfblup_prediction_all,"T15_8_gfblup_prediction_all.rds") +saveRDS(T15_8_gfblup_variances_all,"T15_8_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_1_gblup_prediction_all_1_1000=readRDS(file="T16_1_gblup_prediction_all_1_1000.rds") +T16_1_gblup_prediction_all_1001_2000=readRDS(file="T16_1_gblup_prediction_all_1001_2000.rds") +T16_1_gblup_prediction_all_2001_3000=readRDS(file="T16_1_gblup_prediction_all_2001_3000.rds") +T16_1_gblup_prediction_all_3001_4000=readRDS(file="T16_1_gblup_prediction_all_3001_4000.rds") +T16_1_gblup_prediction_all_4001_5000=readRDS(file="T16_1_gblup_prediction_all_4001_5000.rds") +T16_1_gblup_prediction_all_5001_6000=readRDS(file="T16_1_gblup_prediction_all_5001_6000.rds") +T16_1_gblup_prediction_all_6001_7297=readRDS(file="T16_1_gblup_prediction_all_6001_7297.rds") +T16_1_gblup_prediction_all=c(T16_1_gblup_prediction_all_1_1000,T16_1_gblup_prediction_all_1001_2000,T16_1_gblup_prediction_all_2001_3000,T16_1_gblup_prediction_all_3001_4000,T16_1_gblup_prediction_all_4001_5000,T16_1_gblup_prediction_all_5001_6000,T16_1_gblup_prediction_all_6001_7297) + +T16_1_gblup_variances_all_1_1000=readRDS(file="T16_1_gblup_variances_all_1_1000.rds") +T16_1_gblup_variances_all_1001_2000=readRDS(file="T16_1_gblup_variances_all_1001_2000.rds") +T16_1_gblup_variances_all_2001_3000=readRDS(file="T16_1_gblup_variances_all_2001_3000.rds") +T16_1_gblup_variances_all_3001_4000=readRDS(file="T16_1_gblup_variances_all_3001_4000.rds") +T16_1_gblup_variances_all_4001_5000=readRDS(file="T16_1_gblup_variances_all_4001_5000.rds") +T16_1_gblup_variances_all_5001_6000=readRDS(file="T16_1_gblup_variances_all_5001_6000.rds") +T16_1_gblup_variances_all_6001_7297=readRDS(file="T16_1_gblup_variances_all_6001_7297.rds") +T16_1_gblup_variances_all=c(T16_1_gblup_variances_all_1_1000,T16_1_gblup_variances_all_1001_2000,T16_1_gblup_variances_all_2001_3000,T16_1_gblup_variances_all_3001_4000,T16_1_gblup_variances_all_4001_5000,T16_1_gblup_variances_all_5001_6000,T16_1_gblup_variances_all_6001_7297) + +saveRDS(T16_1_gblup_prediction_all,"T16_1_gblup_prediction_all.rds") +saveRDS(T16_1_gblup_variances_all,"T16_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_1_gfblup_prediction_all_1_1000=readRDS(file="T16_1_gfblup_prediction_all_1_1000.rds") +T16_1_gfblup_prediction_all_1001_2000=readRDS(file="T16_1_gfblup_prediction_all_1001_2000.rds") +T16_1_gfblup_prediction_all_2001_3000=readRDS(file="T16_1_gfblup_prediction_all_2001_3000.rds") +T16_1_gfblup_prediction_all_3001_4000=readRDS(file="T16_1_gfblup_prediction_all_3001_4000.rds") +T16_1_gfblup_prediction_all_4001_5000=readRDS(file="T16_1_gfblup_prediction_all_4001_5000.rds") +T16_1_gfblup_prediction_all_5001_6000=readRDS(file="T16_1_gfblup_prediction_all_5001_6000.rds") +T16_1_gfblup_prediction_all_6001_7297=readRDS(file="T16_1_gfblup_prediction_all_6001_7297.rds") + +T16_1_gfblup_variances_all_1_1000=readRDS(file="T16_1_gfblup_variances_all_1_1000.rds") +T16_1_gfblup_variances_all_1001_2000=readRDS(file="T16_1_gfblup_variances_all_1001_2000.rds") +T16_1_gfblup_variances_all_2001_3000=readRDS(file="T16_1_gfblup_variances_all_2001_3000.rds") +T16_1_gfblup_variances_all_3001_4000=readRDS(file="T16_1_gfblup_variances_all_3001_4000.rds") +T16_1_gfblup_variances_all_4001_5000=readRDS(file="T16_1_gfblup_variances_all_4001_5000.rds") +T16_1_gfblup_variances_all_5001_6000=readRDS(file="T16_1_gfblup_variances_all_5001_6000.rds") +T16_1_gfblup_variances_all_6001_7297=readRDS(file="T16_1_gfblup_variances_all_6001_7297.rds") + +cycles=length(T16_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T16_1_gfblup_variances_all=rep(list(list()),cycles) +T16_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_1_1000[[r]]) + T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_1001_2000[[r]]) + T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_2001_3000[[r]]) + T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_3001_4000[[r]]) + T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_4001_5000[[r]]) + T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_5001_6000[[r]]) + T16_1_gfblup_prediction_all[[r]]<-c(T16_1_gfblup_prediction_all[[r]],T16_1_gfblup_prediction_all_6001_7297[[r]]) + + T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_1_1000[[r]]) + T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_1001_2000[[r]]) + T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_2001_3000[[r]]) + T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_3001_4000[[r]]) + T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_4001_5000[[r]]) + T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_5001_6000[[r]]) + T16_1_gfblup_variances_all[[r]]<-c(T16_1_gfblup_variances_all[[r]],T16_1_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T16_1_gfblup_prediction_all,"T16_1_gfblup_prediction_all.rds") +saveRDS(T16_1_gfblup_variances_all,"T16_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_2_gblup_prediction_all_1_1000=readRDS(file="T16_2_gblup_prediction_all_1_1000.rds") +T16_2_gblup_prediction_all_1001_2000=readRDS(file="T16_2_gblup_prediction_all_1001_2000.rds") +T16_2_gblup_prediction_all_2001_3000=readRDS(file="T16_2_gblup_prediction_all_2001_3000.rds") +T16_2_gblup_prediction_all_3001_4000=readRDS(file="T16_2_gblup_prediction_all_3001_4000.rds") +T16_2_gblup_prediction_all_4001_5000=readRDS(file="T16_2_gblup_prediction_all_4001_5000.rds") +T16_2_gblup_prediction_all_5001_6000=readRDS(file="T16_2_gblup_prediction_all_5001_6000.rds") +T16_2_gblup_prediction_all_6001_7297=readRDS(file="T16_2_gblup_prediction_all_6001_7297.rds") +T16_2_gblup_prediction_all=c(T16_2_gblup_prediction_all_1_1000,T16_2_gblup_prediction_all_1001_2000,T16_2_gblup_prediction_all_2001_3000,T16_2_gblup_prediction_all_3001_4000,T16_2_gblup_prediction_all_4001_5000,T16_2_gblup_prediction_all_5001_6000,T16_2_gblup_prediction_all_6001_7297) + +T16_2_gblup_variances_all_1_1000=readRDS(file="T16_2_gblup_variances_all_1_1000.rds") +T16_2_gblup_variances_all_1001_2000=readRDS(file="T16_2_gblup_variances_all_1001_2000.rds") +T16_2_gblup_variances_all_2001_3000=readRDS(file="T16_2_gblup_variances_all_2001_3000.rds") +T16_2_gblup_variances_all_3001_4000=readRDS(file="T16_2_gblup_variances_all_3001_4000.rds") +T16_2_gblup_variances_all_4001_5000=readRDS(file="T16_2_gblup_variances_all_4001_5000.rds") +T16_2_gblup_variances_all_5001_6000=readRDS(file="T16_2_gblup_variances_all_5001_6000.rds") +T16_2_gblup_variances_all_6001_7297=readRDS(file="T16_2_gblup_variances_all_6001_7297.rds") +T16_2_gblup_variances_all=c(T16_2_gblup_variances_all_1_1000,T16_2_gblup_variances_all_1001_2000,T16_2_gblup_variances_all_2001_3000,T16_2_gblup_variances_all_3001_4000,T16_2_gblup_variances_all_4001_5000,T16_2_gblup_variances_all_5001_6000,T16_2_gblup_variances_all_6001_7297) + +saveRDS(T16_2_gblup_prediction_all,"T16_2_gblup_prediction_all.rds") +saveRDS(T16_2_gblup_variances_all,"T16_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_2_gfblup_prediction_all_1_1000=readRDS(file="T16_2_gfblup_prediction_all_1_1000.rds") +T16_2_gfblup_prediction_all_1001_2000=readRDS(file="T16_2_gfblup_prediction_all_1001_2000.rds") +T16_2_gfblup_prediction_all_2001_3000=readRDS(file="T16_2_gfblup_prediction_all_2001_3000.rds") +T16_2_gfblup_prediction_all_3001_4000=readRDS(file="T16_2_gfblup_prediction_all_3001_4000.rds") +T16_2_gfblup_prediction_all_4001_5000=readRDS(file="T16_2_gfblup_prediction_all_4001_5000.rds") +T16_2_gfblup_prediction_all_5001_6000=readRDS(file="T16_2_gfblup_prediction_all_5001_6000.rds") +T16_2_gfblup_prediction_all_6001_7297=readRDS(file="T16_2_gfblup_prediction_all_6001_7297.rds") + +T16_2_gfblup_variances_all_1_1000=readRDS(file="T16_2_gfblup_variances_all_1_1000.rds") +T16_2_gfblup_variances_all_1001_2000=readRDS(file="T16_2_gfblup_variances_all_1001_2000.rds") +T16_2_gfblup_variances_all_2001_3000=readRDS(file="T16_2_gfblup_variances_all_2001_3000.rds") +T16_2_gfblup_variances_all_3001_4000=readRDS(file="T16_2_gfblup_variances_all_3001_4000.rds") +T16_2_gfblup_variances_all_4001_5000=readRDS(file="T16_2_gfblup_variances_all_4001_5000.rds") +T16_2_gfblup_variances_all_5001_6000=readRDS(file="T16_2_gfblup_variances_all_5001_6000.rds") +T16_2_gfblup_variances_all_6001_7297=readRDS(file="T16_2_gfblup_variances_all_6001_7297.rds") + +cycles=length(T16_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T16_2_gfblup_variances_all=rep(list(list()),cycles) +T16_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_1_1000[[r]]) + T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_1001_2000[[r]]) + T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_2001_3000[[r]]) + T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_3001_4000[[r]]) + T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_4001_5000[[r]]) + T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_5001_6000[[r]]) + T16_2_gfblup_prediction_all[[r]]<-c(T16_2_gfblup_prediction_all[[r]],T16_2_gfblup_prediction_all_6001_7297[[r]]) + + T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_1_1000[[r]]) + T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_1001_2000[[r]]) + T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_2001_3000[[r]]) + T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_3001_4000[[r]]) + T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_4001_5000[[r]]) + T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_5001_6000[[r]]) + T16_2_gfblup_variances_all[[r]]<-c(T16_2_gfblup_variances_all[[r]],T16_2_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T16_2_gfblup_prediction_all,"T16_2_gfblup_prediction_all.rds") +saveRDS(T16_2_gfblup_variances_all,"T16_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_3_gblup_prediction_all_1_1000=readRDS(file="T16_3_gblup_prediction_all_1_1000.rds") +T16_3_gblup_prediction_all_1001_2000=readRDS(file="T16_3_gblup_prediction_all_1001_2000.rds") +T16_3_gblup_prediction_all_2001_3000=readRDS(file="T16_3_gblup_prediction_all_2001_3000.rds") +T16_3_gblup_prediction_all_3001_4000=readRDS(file="T16_3_gblup_prediction_all_3001_4000.rds") +T16_3_gblup_prediction_all_4001_5000=readRDS(file="T16_3_gblup_prediction_all_4001_5000.rds") +T16_3_gblup_prediction_all_5001_6000=readRDS(file="T16_3_gblup_prediction_all_5001_6000.rds") +T16_3_gblup_prediction_all_6001_7297=readRDS(file="T16_3_gblup_prediction_all_6001_7297.rds") +T16_3_gblup_prediction_all=c(T16_3_gblup_prediction_all_1_1000,T16_3_gblup_prediction_all_1001_2000,T16_3_gblup_prediction_all_2001_3000,T16_3_gblup_prediction_all_3001_4000,T16_3_gblup_prediction_all_4001_5000,T16_3_gblup_prediction_all_5001_6000,T16_3_gblup_prediction_all_6001_7297) + +T16_3_gblup_variances_all_1_1000=readRDS(file="T16_3_gblup_variances_all_1_1000.rds") +T16_3_gblup_variances_all_1001_2000=readRDS(file="T16_3_gblup_variances_all_1001_2000.rds") +T16_3_gblup_variances_all_2001_3000=readRDS(file="T16_3_gblup_variances_all_2001_3000.rds") +T16_3_gblup_variances_all_3001_4000=readRDS(file="T16_3_gblup_variances_all_3001_4000.rds") +T16_3_gblup_variances_all_4001_5000=readRDS(file="T16_3_gblup_variances_all_4001_5000.rds") +T16_3_gblup_variances_all_5001_6000=readRDS(file="T16_3_gblup_variances_all_5001_6000.rds") +T16_3_gblup_variances_all_6001_7297=readRDS(file="T16_3_gblup_variances_all_6001_7297.rds") +T16_3_gblup_variances_all=c(T16_3_gblup_variances_all_1_1000,T16_3_gblup_variances_all_1001_2000,T16_3_gblup_variances_all_2001_3000,T16_3_gblup_variances_all_3001_4000,T16_3_gblup_variances_all_4001_5000,T16_3_gblup_variances_all_5001_6000,T16_3_gblup_variances_all_6001_7297) + +saveRDS(T16_3_gblup_prediction_all,"T16_3_gblup_prediction_all.rds") +saveRDS(T16_3_gblup_variances_all,"T16_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_3_gfblup_prediction_all_1_1000=readRDS(file="T16_3_gfblup_prediction_all_1_1000.rds") +T16_3_gfblup_prediction_all_1001_2000=readRDS(file="T16_3_gfblup_prediction_all_1001_2000.rds") +T16_3_gfblup_prediction_all_2001_3000=readRDS(file="T16_3_gfblup_prediction_all_2001_3000.rds") +T16_3_gfblup_prediction_all_3001_4000=readRDS(file="T16_3_gfblup_prediction_all_3001_4000.rds") +T16_3_gfblup_prediction_all_4001_5000=readRDS(file="T16_3_gfblup_prediction_all_4001_5000.rds") +T16_3_gfblup_prediction_all_5001_6000=readRDS(file="T16_3_gfblup_prediction_all_5001_6000.rds") +T16_3_gfblup_prediction_all_6001_7297=readRDS(file="T16_3_gfblup_prediction_all_6001_7297.rds") + +T16_3_gfblup_variances_all_1_1000=readRDS(file="T16_3_gfblup_variances_all_1_1000.rds") +T16_3_gfblup_variances_all_1001_2000=readRDS(file="T16_3_gfblup_variances_all_1001_2000.rds") +T16_3_gfblup_variances_all_2001_3000=readRDS(file="T16_3_gfblup_variances_all_2001_3000.rds") +T16_3_gfblup_variances_all_3001_4000=readRDS(file="T16_3_gfblup_variances_all_3001_4000.rds") +T16_3_gfblup_variances_all_4001_5000=readRDS(file="T16_3_gfblup_variances_all_4001_5000.rds") +T16_3_gfblup_variances_all_5001_6000=readRDS(file="T16_3_gfblup_variances_all_5001_6000.rds") +T16_3_gfblup_variances_all_6001_7297=readRDS(file="T16_3_gfblup_variances_all_6001_7297.rds") + +cycles=length(T16_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T16_3_gfblup_variances_all=rep(list(list()),cycles) +T16_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_1_1000[[r]]) + T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_1001_2000[[r]]) + T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_2001_3000[[r]]) + T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_3001_4000[[r]]) + T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_4001_5000[[r]]) + T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_5001_6000[[r]]) + T16_3_gfblup_prediction_all[[r]]<-c(T16_3_gfblup_prediction_all[[r]],T16_3_gfblup_prediction_all_6001_7297[[r]]) + + T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_1_1000[[r]]) + T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_1001_2000[[r]]) + T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_2001_3000[[r]]) + T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_3001_4000[[r]]) + T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_4001_5000[[r]]) + T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_5001_6000[[r]]) + T16_3_gfblup_variances_all[[r]]<-c(T16_3_gfblup_variances_all[[r]],T16_3_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T16_3_gfblup_prediction_all,"T16_3_gfblup_prediction_all.rds") +saveRDS(T16_3_gfblup_variances_all,"T16_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_4_gblup_prediction_all_1_1000=readRDS(file="T16_4_gblup_prediction_all_1_1000.rds") +T16_4_gblup_prediction_all_1001_2000=readRDS(file="T16_4_gblup_prediction_all_1001_2000.rds") +T16_4_gblup_prediction_all_2001_3000=readRDS(file="T16_4_gblup_prediction_all_2001_3000.rds") +T16_4_gblup_prediction_all_3001_4000=readRDS(file="T16_4_gblup_prediction_all_3001_4000.rds") +T16_4_gblup_prediction_all_4001_5000=readRDS(file="T16_4_gblup_prediction_all_4001_5000.rds") +T16_4_gblup_prediction_all_5001_6000=readRDS(file="T16_4_gblup_prediction_all_5001_6000.rds") +T16_4_gblup_prediction_all_6001_7297=readRDS(file="T16_4_gblup_prediction_all_6001_7297.rds") +T16_4_gblup_prediction_all=c(T16_4_gblup_prediction_all_1_1000,T16_4_gblup_prediction_all_1001_2000,T16_4_gblup_prediction_all_2001_3000,T16_4_gblup_prediction_all_3001_4000,T16_4_gblup_prediction_all_4001_5000,T16_4_gblup_prediction_all_5001_6000,T16_4_gblup_prediction_all_6001_7297) + +T16_4_gblup_variances_all_1_1000=readRDS(file="T16_4_gblup_variances_all_1_1000.rds") +T16_4_gblup_variances_all_1001_2000=readRDS(file="T16_4_gblup_variances_all_1001_2000.rds") +T16_4_gblup_variances_all_2001_3000=readRDS(file="T16_4_gblup_variances_all_2001_3000.rds") +T16_4_gblup_variances_all_3001_4000=readRDS(file="T16_4_gblup_variances_all_3001_4000.rds") +T16_4_gblup_variances_all_4001_5000=readRDS(file="T16_4_gblup_variances_all_4001_5000.rds") +T16_4_gblup_variances_all_5001_6000=readRDS(file="T16_4_gblup_variances_all_5001_6000.rds") +T16_4_gblup_variances_all_6001_7297=readRDS(file="T16_4_gblup_variances_all_6001_7297.rds") +T16_4_gblup_variances_all=c(T16_4_gblup_variances_all_1_1000,T16_4_gblup_variances_all_1001_2000,T16_4_gblup_variances_all_2001_3000,T16_4_gblup_variances_all_3001_4000,T16_4_gblup_variances_all_4001_5000,T16_4_gblup_variances_all_5001_6000,T16_4_gblup_variances_all_6001_7297) + +saveRDS(T16_4_gblup_prediction_all,"T16_4_gblup_prediction_all.rds") +saveRDS(T16_4_gblup_variances_all,"T16_4_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_4_gfblup_prediction_all_1_1000=readRDS(file="T16_4_gfblup_prediction_all_1_1000.rds") +T16_4_gfblup_prediction_all_1001_2000=readRDS(file="T16_4_gfblup_prediction_all_1001_2000.rds") +T16_4_gfblup_prediction_all_2001_3000=readRDS(file="T16_4_gfblup_prediction_all_2001_3000.rds") +T16_4_gfblup_prediction_all_3001_4000=readRDS(file="T16_4_gfblup_prediction_all_3001_4000.rds") +T16_4_gfblup_prediction_all_4001_5000=readRDS(file="T16_4_gfblup_prediction_all_4001_5000.rds") +T16_4_gfblup_prediction_all_5001_6000=readRDS(file="T16_4_gfblup_prediction_all_5001_6000.rds") +T16_4_gfblup_prediction_all_6001_7297=readRDS(file="T16_4_gfblup_prediction_all_6001_7297.rds") + +T16_4_gfblup_variances_all_1_1000=readRDS(file="T16_4_gfblup_variances_all_1_1000.rds") +T16_4_gfblup_variances_all_1001_2000=readRDS(file="T16_4_gfblup_variances_all_1001_2000.rds") +T16_4_gfblup_variances_all_2001_3000=readRDS(file="T16_4_gfblup_variances_all_2001_3000.rds") +T16_4_gfblup_variances_all_3001_4000=readRDS(file="T16_4_gfblup_variances_all_3001_4000.rds") +T16_4_gfblup_variances_all_4001_5000=readRDS(file="T16_4_gfblup_variances_all_4001_5000.rds") +T16_4_gfblup_variances_all_5001_6000=readRDS(file="T16_4_gfblup_variances_all_5001_6000.rds") +T16_4_gfblup_variances_all_6001_7297=readRDS(file="T16_4_gfblup_variances_all_6001_7297.rds") + +cycles=length(T16_4_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T16_4_gfblup_variances_all=rep(list(list()),cycles) +T16_4_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_1_1000[[r]]) + T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_1001_2000[[r]]) + T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_2001_3000[[r]]) + T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_3001_4000[[r]]) + T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_4001_5000[[r]]) + T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_5001_6000[[r]]) + T16_4_gfblup_prediction_all[[r]]<-c(T16_4_gfblup_prediction_all[[r]],T16_4_gfblup_prediction_all_6001_7297[[r]]) + + T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_1_1000[[r]]) + T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_1001_2000[[r]]) + T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_2001_3000[[r]]) + T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_3001_4000[[r]]) + T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_4001_5000[[r]]) + T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_5001_6000[[r]]) + T16_4_gfblup_variances_all[[r]]<-c(T16_4_gfblup_variances_all[[r]],T16_4_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T16_4_gfblup_prediction_all,"T16_4_gfblup_prediction_all.rds") +saveRDS(T16_4_gfblup_variances_all,"T16_4_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_5_gblup_prediction_all_1_1000=readRDS(file="T16_5_gblup_prediction_all_1_1000.rds") +T16_5_gblup_prediction_all_1001_2000=readRDS(file="T16_5_gblup_prediction_all_1001_2000.rds") +T16_5_gblup_prediction_all_2001_3000=readRDS(file="T16_5_gblup_prediction_all_2001_3000.rds") +T16_5_gblup_prediction_all_3001_4000=readRDS(file="T16_5_gblup_prediction_all_3001_4000.rds") +T16_5_gblup_prediction_all_4001_5000=readRDS(file="T16_5_gblup_prediction_all_4001_5000.rds") +T16_5_gblup_prediction_all_5001_6000=readRDS(file="T16_5_gblup_prediction_all_5001_6000.rds") +T16_5_gblup_prediction_all_6001_7297=readRDS(file="T16_5_gblup_prediction_all_6001_7297.rds") +T16_5_gblup_prediction_all=c(T16_5_gblup_prediction_all_1_1000,T16_5_gblup_prediction_all_1001_2000,T16_5_gblup_prediction_all_2001_3000,T16_5_gblup_prediction_all_3001_4000,T16_5_gblup_prediction_all_4001_5000,T16_5_gblup_prediction_all_5001_6000,T16_5_gblup_prediction_all_6001_7297) + +T16_5_gblup_variances_all_1_1000=readRDS(file="T16_5_gblup_variances_all_1_1000.rds") +T16_5_gblup_variances_all_1001_2000=readRDS(file="T16_5_gblup_variances_all_1001_2000.rds") +T16_5_gblup_variances_all_2001_3000=readRDS(file="T16_5_gblup_variances_all_2001_3000.rds") +T16_5_gblup_variances_all_3001_4000=readRDS(file="T16_5_gblup_variances_all_3001_4000.rds") +T16_5_gblup_variances_all_4001_5000=readRDS(file="T16_5_gblup_variances_all_4001_5000.rds") +T16_5_gblup_variances_all_5001_6000=readRDS(file="T16_5_gblup_variances_all_5001_6000.rds") +T16_5_gblup_variances_all_6001_7297=readRDS(file="T16_5_gblup_variances_all_6001_7297.rds") +T16_5_gblup_variances_all=c(T16_5_gblup_variances_all_1_1000,T16_5_gblup_variances_all_1001_2000,T16_5_gblup_variances_all_2001_3000,T16_5_gblup_variances_all_3001_4000,T16_5_gblup_variances_all_4001_5000,T16_5_gblup_variances_all_5001_6000,T16_5_gblup_variances_all_6001_7297) + +saveRDS(T16_5_gblup_prediction_all,"T16_5_gblup_prediction_all.rds") +saveRDS(T16_5_gblup_variances_all,"T16_5_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_5_gfblup_prediction_all_1_1000=readRDS(file="T16_5_gfblup_prediction_all_1_1000.rds") +T16_5_gfblup_prediction_all_1001_2000=readRDS(file="T16_5_gfblup_prediction_all_1001_2000.rds") +T16_5_gfblup_prediction_all_2001_3000=readRDS(file="T16_5_gfblup_prediction_all_2001_3000.rds") +T16_5_gfblup_prediction_all_3001_4000=readRDS(file="T16_5_gfblup_prediction_all_3001_4000.rds") +T16_5_gfblup_prediction_all_4001_5000=readRDS(file="T16_5_gfblup_prediction_all_4001_5000.rds") +T16_5_gfblup_prediction_all_5001_6000=readRDS(file="T16_5_gfblup_prediction_all_5001_6000.rds") +T16_5_gfblup_prediction_all_6001_7297=readRDS(file="T16_5_gfblup_prediction_all_6001_7297.rds") + +T16_5_gfblup_variances_all_1_1000=readRDS(file="T16_5_gfblup_variances_all_1_1000.rds") +T16_5_gfblup_variances_all_1001_2000=readRDS(file="T16_5_gfblup_variances_all_1001_2000.rds") +T16_5_gfblup_variances_all_2001_3000=readRDS(file="T16_5_gfblup_variances_all_2001_3000.rds") +T16_5_gfblup_variances_all_3001_4000=readRDS(file="T16_5_gfblup_variances_all_3001_4000.rds") +T16_5_gfblup_variances_all_4001_5000=readRDS(file="T16_5_gfblup_variances_all_4001_5000.rds") +T16_5_gfblup_variances_all_5001_6000=readRDS(file="T16_5_gfblup_variances_all_5001_6000.rds") +T16_5_gfblup_variances_all_6001_7297=readRDS(file="T16_5_gfblup_variances_all_6001_7297.rds") + +cycles=length(T16_5_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T16_5_gfblup_variances_all=rep(list(list()),cycles) +T16_5_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_1_1000[[r]]) + T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_1001_2000[[r]]) + T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_2001_3000[[r]]) + T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_3001_4000[[r]]) + T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_4001_5000[[r]]) + T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_5001_6000[[r]]) + T16_5_gfblup_prediction_all[[r]]<-c(T16_5_gfblup_prediction_all[[r]],T16_5_gfblup_prediction_all_6001_7297[[r]]) + + T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_1_1000[[r]]) + T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_1001_2000[[r]]) + T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_2001_3000[[r]]) + T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_3001_4000[[r]]) + T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_4001_5000[[r]]) + T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_5001_6000[[r]]) + T16_5_gfblup_variances_all[[r]]<-c(T16_5_gfblup_variances_all[[r]],T16_5_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T16_5_gfblup_prediction_all,"T16_5_gfblup_prediction_all.rds") +saveRDS(T16_5_gfblup_variances_all,"T16_5_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_6_gblup_prediction_all_1_1000=readRDS(file="T16_6_gblup_prediction_all_1_1000.rds") +T16_6_gblup_prediction_all_1001_2000=readRDS(file="T16_6_gblup_prediction_all_1001_2000.rds") +T16_6_gblup_prediction_all_2001_3000=readRDS(file="T16_6_gblup_prediction_all_2001_3000.rds") +T16_6_gblup_prediction_all_3001_4000=readRDS(file="T16_6_gblup_prediction_all_3001_4000.rds") +T16_6_gblup_prediction_all_4001_5000=readRDS(file="T16_6_gblup_prediction_all_4001_5000.rds") +T16_6_gblup_prediction_all_5001_6000=readRDS(file="T16_6_gblup_prediction_all_5001_6000.rds") +T16_6_gblup_prediction_all_6001_7297=readRDS(file="T16_6_gblup_prediction_all_6001_7297.rds") +T16_6_gblup_prediction_all=c(T16_6_gblup_prediction_all_1_1000,T16_6_gblup_prediction_all_1001_2000,T16_6_gblup_prediction_all_2001_3000,T16_6_gblup_prediction_all_3001_4000,T16_6_gblup_prediction_all_4001_5000,T16_6_gblup_prediction_all_5001_6000,T16_6_gblup_prediction_all_6001_7297) + +T16_6_gblup_variances_all_1_1000=readRDS(file="T16_6_gblup_variances_all_1_1000.rds") +T16_6_gblup_variances_all_1001_2000=readRDS(file="T16_6_gblup_variances_all_1001_2000.rds") +T16_6_gblup_variances_all_2001_3000=readRDS(file="T16_6_gblup_variances_all_2001_3000.rds") +T16_6_gblup_variances_all_3001_4000=readRDS(file="T16_6_gblup_variances_all_3001_4000.rds") +T16_6_gblup_variances_all_4001_5000=readRDS(file="T16_6_gblup_variances_all_4001_5000.rds") +T16_6_gblup_variances_all_5001_6000=readRDS(file="T16_6_gblup_variances_all_5001_6000.rds") +T16_6_gblup_variances_all_6001_7297=readRDS(file="T16_6_gblup_variances_all_6001_7297.rds") +T16_6_gblup_variances_all=c(T16_6_gblup_variances_all_1_1000,T16_6_gblup_variances_all_1001_2000,T16_6_gblup_variances_all_2001_3000,T16_6_gblup_variances_all_3001_4000,T16_6_gblup_variances_all_4001_5000,T16_6_gblup_variances_all_5001_6000,T16_6_gblup_variances_all_6001_7297) + +saveRDS(T16_6_gblup_prediction_all,"T16_6_gblup_prediction_all.rds") +saveRDS(T16_6_gblup_variances_all,"T16_6_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_6_gfblup_prediction_all_1_1000=readRDS(file="T16_6_gfblup_prediction_all_1_1000.rds") +T16_6_gfblup_prediction_all_1001_2000=readRDS(file="T16_6_gfblup_prediction_all_1001_2000.rds") +T16_6_gfblup_prediction_all_2001_3000=readRDS(file="T16_6_gfblup_prediction_all_2001_3000.rds") +T16_6_gfblup_prediction_all_3001_4000=readRDS(file="T16_6_gfblup_prediction_all_3001_4000.rds") +T16_6_gfblup_prediction_all_4001_5000=readRDS(file="T16_6_gfblup_prediction_all_4001_5000.rds") +T16_6_gfblup_prediction_all_5001_6000=readRDS(file="T16_6_gfblup_prediction_all_5001_6000.rds") +T16_6_gfblup_prediction_all_6001_7297=readRDS(file="T16_6_gfblup_prediction_all_6001_7297.rds") + +T16_6_gfblup_variances_all_1_1000=readRDS(file="T16_6_gfblup_variances_all_1_1000.rds") +T16_6_gfblup_variances_all_1001_2000=readRDS(file="T16_6_gfblup_variances_all_1001_2000.rds") +T16_6_gfblup_variances_all_2001_3000=readRDS(file="T16_6_gfblup_variances_all_2001_3000.rds") +T16_6_gfblup_variances_all_3001_4000=readRDS(file="T16_6_gfblup_variances_all_3001_4000.rds") +T16_6_gfblup_variances_all_4001_5000=readRDS(file="T16_6_gfblup_variances_all_4001_5000.rds") +T16_6_gfblup_variances_all_5001_6000=readRDS(file="T16_6_gfblup_variances_all_5001_6000.rds") +T16_6_gfblup_variances_all_6001_7297=readRDS(file="T16_6_gfblup_variances_all_6001_7297.rds") + +cycles=length(T16_6_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T16_6_gfblup_variances_all=rep(list(list()),cycles) +T16_6_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_1_1000[[r]]) + T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_1001_2000[[r]]) + T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_2001_3000[[r]]) + T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_3001_4000[[r]]) + T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_4001_5000[[r]]) + T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_5001_6000[[r]]) + T16_6_gfblup_prediction_all[[r]]<-c(T16_6_gfblup_prediction_all[[r]],T16_6_gfblup_prediction_all_6001_7297[[r]]) + + T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_1_1000[[r]]) + T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_1001_2000[[r]]) + T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_2001_3000[[r]]) + T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_3001_4000[[r]]) + T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_4001_5000[[r]]) + T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_5001_6000[[r]]) + T16_6_gfblup_variances_all[[r]]<-c(T16_6_gfblup_variances_all[[r]],T16_6_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T16_6_gfblup_prediction_all,"T16_6_gfblup_prediction_all.rds") +saveRDS(T16_6_gfblup_variances_all,"T16_6_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_7_gblup_prediction_all_1_1000=readRDS(file="T16_7_gblup_prediction_all_1_1000.rds") +T16_7_gblup_prediction_all_1001_2000=readRDS(file="T16_7_gblup_prediction_all_1001_2000.rds") +T16_7_gblup_prediction_all_2001_3000=readRDS(file="T16_7_gblup_prediction_all_2001_3000.rds") +T16_7_gblup_prediction_all_3001_4000=readRDS(file="T16_7_gblup_prediction_all_3001_4000.rds") +T16_7_gblup_prediction_all_4001_5000=readRDS(file="T16_7_gblup_prediction_all_4001_5000.rds") +T16_7_gblup_prediction_all_5001_6000=readRDS(file="T16_7_gblup_prediction_all_5001_6000.rds") +T16_7_gblup_prediction_all_6001_7297=readRDS(file="T16_7_gblup_prediction_all_6001_7297.rds") +T16_7_gblup_prediction_all=c(T16_7_gblup_prediction_all_1_1000,T16_7_gblup_prediction_all_1001_2000,T16_7_gblup_prediction_all_2001_3000,T16_7_gblup_prediction_all_3001_4000,T16_7_gblup_prediction_all_4001_5000,T16_7_gblup_prediction_all_5001_6000,T16_7_gblup_prediction_all_6001_7297) + +T16_7_gblup_variances_all_1_1000=readRDS(file="T16_7_gblup_variances_all_1_1000.rds") +T16_7_gblup_variances_all_1001_2000=readRDS(file="T16_7_gblup_variances_all_1001_2000.rds") +T16_7_gblup_variances_all_2001_3000=readRDS(file="T16_7_gblup_variances_all_2001_3000.rds") +T16_7_gblup_variances_all_3001_4000=readRDS(file="T16_7_gblup_variances_all_3001_4000.rds") +T16_7_gblup_variances_all_4001_5000=readRDS(file="T16_7_gblup_variances_all_4001_5000.rds") +T16_7_gblup_variances_all_5001_6000=readRDS(file="T16_7_gblup_variances_all_5001_6000.rds") +T16_7_gblup_variances_all_6001_7297=readRDS(file="T16_7_gblup_variances_all_6001_7297.rds") +T16_7_gblup_variances_all=c(T16_7_gblup_variances_all_1_1000,T16_7_gblup_variances_all_1001_2000,T16_7_gblup_variances_all_2001_3000,T16_7_gblup_variances_all_3001_4000,T16_7_gblup_variances_all_4001_5000,T16_7_gblup_variances_all_5001_6000,T16_7_gblup_variances_all_6001_7297) + +saveRDS(T16_7_gblup_prediction_all,"T16_7_gblup_prediction_all.rds") +saveRDS(T16_7_gblup_variances_all,"T16_7_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_7_gfblup_prediction_all_1_1000=readRDS(file="T16_7_gfblup_prediction_all_1_1000.rds") +T16_7_gfblup_prediction_all_1001_2000=readRDS(file="T16_7_gfblup_prediction_all_1001_2000.rds") +T16_7_gfblup_prediction_all_2001_3000=readRDS(file="T16_7_gfblup_prediction_all_2001_3000.rds") +T16_7_gfblup_prediction_all_3001_4000=readRDS(file="T16_7_gfblup_prediction_all_3001_4000.rds") +T16_7_gfblup_prediction_all_4001_5000=readRDS(file="T16_7_gfblup_prediction_all_4001_5000.rds") +T16_7_gfblup_prediction_all_5001_6000=readRDS(file="T16_7_gfblup_prediction_all_5001_6000.rds") +T16_7_gfblup_prediction_all_6001_7297=readRDS(file="T16_7_gfblup_prediction_all_6001_7297.rds") + +T16_7_gfblup_variances_all_1_1000=readRDS(file="T16_7_gfblup_variances_all_1_1000.rds") +T16_7_gfblup_variances_all_1001_2000=readRDS(file="T16_7_gfblup_variances_all_1001_2000.rds") +T16_7_gfblup_variances_all_2001_3000=readRDS(file="T16_7_gfblup_variances_all_2001_3000.rds") +T16_7_gfblup_variances_all_3001_4000=readRDS(file="T16_7_gfblup_variances_all_3001_4000.rds") +T16_7_gfblup_variances_all_4001_5000=readRDS(file="T16_7_gfblup_variances_all_4001_5000.rds") +T16_7_gfblup_variances_all_5001_6000=readRDS(file="T16_7_gfblup_variances_all_5001_6000.rds") +T16_7_gfblup_variances_all_6001_7297=readRDS(file="T16_7_gfblup_variances_all_6001_7297.rds") + +cycles=length(T16_7_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T16_7_gfblup_variances_all=rep(list(list()),cycles) +T16_7_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_1_1000[[r]]) + T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_1001_2000[[r]]) + T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_2001_3000[[r]]) + T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_3001_4000[[r]]) + T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_4001_5000[[r]]) + T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_5001_6000[[r]]) + T16_7_gfblup_prediction_all[[r]]<-c(T16_7_gfblup_prediction_all[[r]],T16_7_gfblup_prediction_all_6001_7297[[r]]) + + T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_1_1000[[r]]) + T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_1001_2000[[r]]) + T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_2001_3000[[r]]) + T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_3001_4000[[r]]) + T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_4001_5000[[r]]) + T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_5001_6000[[r]]) + T16_7_gfblup_variances_all[[r]]<-c(T16_7_gfblup_variances_all[[r]],T16_7_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T16_7_gfblup_prediction_all,"T16_7_gfblup_prediction_all.rds") +saveRDS(T16_7_gfblup_variances_all,"T16_7_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_8_gblup_prediction_all_1_1000=readRDS(file="T16_8_gblup_prediction_all_1_1000.rds") +T16_8_gblup_prediction_all_1001_2000=readRDS(file="T16_8_gblup_prediction_all_1001_2000.rds") +T16_8_gblup_prediction_all_2001_3000=readRDS(file="T16_8_gblup_prediction_all_2001_3000.rds") +T16_8_gblup_prediction_all_3001_4000=readRDS(file="T16_8_gblup_prediction_all_3001_4000.rds") +T16_8_gblup_prediction_all_4001_5000=readRDS(file="T16_8_gblup_prediction_all_4001_5000.rds") +T16_8_gblup_prediction_all_5001_6000=readRDS(file="T16_8_gblup_prediction_all_5001_6000.rds") +T16_8_gblup_prediction_all_6001_7297=readRDS(file="T16_8_gblup_prediction_all_6001_7297.rds") +T16_8_gblup_prediction_all=c(T16_8_gblup_prediction_all_1_1000,T16_8_gblup_prediction_all_1001_2000,T16_8_gblup_prediction_all_2001_3000,T16_8_gblup_prediction_all_3001_4000,T16_8_gblup_prediction_all_4001_5000,T16_8_gblup_prediction_all_5001_6000,T16_8_gblup_prediction_all_6001_7297) + +T16_8_gblup_variances_all_1_1000=readRDS(file="T16_8_gblup_variances_all_1_1000.rds") +T16_8_gblup_variances_all_1001_2000=readRDS(file="T16_8_gblup_variances_all_1001_2000.rds") +T16_8_gblup_variances_all_2001_3000=readRDS(file="T16_8_gblup_variances_all_2001_3000.rds") +T16_8_gblup_variances_all_3001_4000=readRDS(file="T16_8_gblup_variances_all_3001_4000.rds") +T16_8_gblup_variances_all_4001_5000=readRDS(file="T16_8_gblup_variances_all_4001_5000.rds") +T16_8_gblup_variances_all_5001_6000=readRDS(file="T16_8_gblup_variances_all_5001_6000.rds") +T16_8_gblup_variances_all_6001_7297=readRDS(file="T16_8_gblup_variances_all_6001_7297.rds") +T16_8_gblup_variances_all=c(T16_8_gblup_variances_all_1_1000,T16_8_gblup_variances_all_1001_2000,T16_8_gblup_variances_all_2001_3000,T16_8_gblup_variances_all_3001_4000,T16_8_gblup_variances_all_4001_5000,T16_8_gblup_variances_all_5001_6000,T16_8_gblup_variances_all_6001_7297) + +saveRDS(T16_8_gblup_prediction_all,"T16_8_gblup_prediction_all.rds") +saveRDS(T16_8_gblup_variances_all,"T16_8_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T16_8_gfblup_prediction_all_1_1000=readRDS(file="T16_8_gfblup_prediction_all_1_1000.rds") +T16_8_gfblup_prediction_all_1001_2000=readRDS(file="T16_8_gfblup_prediction_all_1001_2000.rds") +T16_8_gfblup_prediction_all_2001_3000=readRDS(file="T16_8_gfblup_prediction_all_2001_3000.rds") +T16_8_gfblup_prediction_all_3001_4000=readRDS(file="T16_8_gfblup_prediction_all_3001_4000.rds") +T16_8_gfblup_prediction_all_4001_5000=readRDS(file="T16_8_gfblup_prediction_all_4001_5000.rds") +T16_8_gfblup_prediction_all_5001_6000=readRDS(file="T16_8_gfblup_prediction_all_5001_6000.rds") +T16_8_gfblup_prediction_all_6001_7297=readRDS(file="T16_8_gfblup_prediction_all_6001_7297.rds") + +T16_8_gfblup_variances_all_1_1000=readRDS(file="T16_8_gfblup_variances_all_1_1000.rds") +T16_8_gfblup_variances_all_1001_2000=readRDS(file="T16_8_gfblup_variances_all_1001_2000.rds") +T16_8_gfblup_variances_all_2001_3000=readRDS(file="T16_8_gfblup_variances_all_2001_3000.rds") +T16_8_gfblup_variances_all_3001_4000=readRDS(file="T16_8_gfblup_variances_all_3001_4000.rds") +T16_8_gfblup_variances_all_4001_5000=readRDS(file="T16_8_gfblup_variances_all_4001_5000.rds") +T16_8_gfblup_variances_all_5001_6000=readRDS(file="T16_8_gfblup_variances_all_5001_6000.rds") +T16_8_gfblup_variances_all_6001_7297=readRDS(file="T16_8_gfblup_variances_all_6001_7297.rds") + +cycles=length(T16_8_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T16_8_gfblup_variances_all=rep(list(list()),cycles) +T16_8_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_1_1000[[r]]) + T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_1001_2000[[r]]) + T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_2001_3000[[r]]) + T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_3001_4000[[r]]) + T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_4001_5000[[r]]) + T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_5001_6000[[r]]) + T16_8_gfblup_prediction_all[[r]]<-c(T16_8_gfblup_prediction_all[[r]],T16_8_gfblup_prediction_all_6001_7297[[r]]) + + T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_1_1000[[r]]) + T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_1001_2000[[r]]) + T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_2001_3000[[r]]) + T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_3001_4000[[r]]) + T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_4001_5000[[r]]) + T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_5001_6000[[r]]) + T16_8_gfblup_variances_all[[r]]<-c(T16_8_gfblup_variances_all[[r]],T16_8_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T16_8_gfblup_prediction_all,"T16_8_gfblup_prediction_all.rds") +saveRDS(T16_8_gfblup_variances_all,"T16_8_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_1_gblup_prediction_all_1_1000=readRDS(file="T17_1_gblup_prediction_all_1_1000.rds") +T17_1_gblup_prediction_all_1001_2000=readRDS(file="T17_1_gblup_prediction_all_1001_2000.rds") +T17_1_gblup_prediction_all_2001_3000=readRDS(file="T17_1_gblup_prediction_all_2001_3000.rds") +T17_1_gblup_prediction_all_3001_4000=readRDS(file="T17_1_gblup_prediction_all_3001_4000.rds") +T17_1_gblup_prediction_all_4001_5000=readRDS(file="T17_1_gblup_prediction_all_4001_5000.rds") +T17_1_gblup_prediction_all_5001_6000=readRDS(file="T17_1_gblup_prediction_all_5001_6000.rds") +T17_1_gblup_prediction_all_6001_7297=readRDS(file="T17_1_gblup_prediction_all_6001_7297.rds") +T17_1_gblup_prediction_all=c(T17_1_gblup_prediction_all_1_1000,T17_1_gblup_prediction_all_1001_2000,T17_1_gblup_prediction_all_2001_3000,T17_1_gblup_prediction_all_3001_4000,T17_1_gblup_prediction_all_4001_5000,T17_1_gblup_prediction_all_5001_6000,T17_1_gblup_prediction_all_6001_7297) + +T17_1_gblup_variances_all_1_1000=readRDS(file="T17_1_gblup_variances_all_1_1000.rds") +T17_1_gblup_variances_all_1001_2000=readRDS(file="T17_1_gblup_variances_all_1001_2000.rds") +T17_1_gblup_variances_all_2001_3000=readRDS(file="T17_1_gblup_variances_all_2001_3000.rds") +T17_1_gblup_variances_all_3001_4000=readRDS(file="T17_1_gblup_variances_all_3001_4000.rds") +T17_1_gblup_variances_all_4001_5000=readRDS(file="T17_1_gblup_variances_all_4001_5000.rds") +T17_1_gblup_variances_all_5001_6000=readRDS(file="T17_1_gblup_variances_all_5001_6000.rds") +T17_1_gblup_variances_all_6001_7297=readRDS(file="T17_1_gblup_variances_all_6001_7297.rds") +T17_1_gblup_variances_all=c(T17_1_gblup_variances_all_1_1000,T17_1_gblup_variances_all_1001_2000,T17_1_gblup_variances_all_2001_3000,T17_1_gblup_variances_all_3001_4000,T17_1_gblup_variances_all_4001_5000,T17_1_gblup_variances_all_5001_6000,T17_1_gblup_variances_all_6001_7297) + +saveRDS(T17_1_gblup_prediction_all,"T17_1_gblup_prediction_all.rds") +saveRDS(T17_1_gblup_variances_all,"T17_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_1_gfblup_prediction_all_1_1000=readRDS(file="T17_1_gfblup_prediction_all_1_1000.rds") +T17_1_gfblup_prediction_all_1001_2000=readRDS(file="T17_1_gfblup_prediction_all_1001_2000.rds") +T17_1_gfblup_prediction_all_2001_3000=readRDS(file="T17_1_gfblup_prediction_all_2001_3000.rds") +T17_1_gfblup_prediction_all_3001_4000=readRDS(file="T17_1_gfblup_prediction_all_3001_4000.rds") +T17_1_gfblup_prediction_all_4001_5000=readRDS(file="T17_1_gfblup_prediction_all_4001_5000.rds") +T17_1_gfblup_prediction_all_5001_6000=readRDS(file="T17_1_gfblup_prediction_all_5001_6000.rds") +T17_1_gfblup_prediction_all_6001_7297=readRDS(file="T17_1_gfblup_prediction_all_6001_7297.rds") + +T17_1_gfblup_variances_all_1_1000=readRDS(file="T17_1_gfblup_variances_all_1_1000.rds") +T17_1_gfblup_variances_all_1001_2000=readRDS(file="T17_1_gfblup_variances_all_1001_2000.rds") +T17_1_gfblup_variances_all_2001_3000=readRDS(file="T17_1_gfblup_variances_all_2001_3000.rds") +T17_1_gfblup_variances_all_3001_4000=readRDS(file="T17_1_gfblup_variances_all_3001_4000.rds") +T17_1_gfblup_variances_all_4001_5000=readRDS(file="T17_1_gfblup_variances_all_4001_5000.rds") +T17_1_gfblup_variances_all_5001_6000=readRDS(file="T17_1_gfblup_variances_all_5001_6000.rds") +T17_1_gfblup_variances_all_6001_7297=readRDS(file="T17_1_gfblup_variances_all_6001_7297.rds") + +cycles=length(T17_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T17_1_gfblup_variances_all=rep(list(list()),cycles) +T17_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_1_1000[[r]]) + T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_1001_2000[[r]]) + T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_2001_3000[[r]]) + T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_3001_4000[[r]]) + T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_4001_5000[[r]]) + T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_5001_6000[[r]]) + T17_1_gfblup_prediction_all[[r]]<-c(T17_1_gfblup_prediction_all[[r]],T17_1_gfblup_prediction_all_6001_7297[[r]]) + + T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_1_1000[[r]]) + T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_1001_2000[[r]]) + T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_2001_3000[[r]]) + T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_3001_4000[[r]]) + T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_4001_5000[[r]]) + T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_5001_6000[[r]]) + T17_1_gfblup_variances_all[[r]]<-c(T17_1_gfblup_variances_all[[r]],T17_1_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T17_1_gfblup_prediction_all,"T17_1_gfblup_prediction_all.rds") +saveRDS(T17_1_gfblup_variances_all,"T17_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_2_gblup_prediction_all_1_1000=readRDS(file="T17_2_gblup_prediction_all_1_1000.rds") +T17_2_gblup_prediction_all_1001_2000=readRDS(file="T17_2_gblup_prediction_all_1001_2000.rds") +T17_2_gblup_prediction_all_2001_3000=readRDS(file="T17_2_gblup_prediction_all_2001_3000.rds") +T17_2_gblup_prediction_all_3001_4000=readRDS(file="T17_2_gblup_prediction_all_3001_4000.rds") +T17_2_gblup_prediction_all_4001_5000=readRDS(file="T17_2_gblup_prediction_all_4001_5000.rds") +T17_2_gblup_prediction_all_5001_6000=readRDS(file="T17_2_gblup_prediction_all_5001_6000.rds") +T17_2_gblup_prediction_all_6001_7297=readRDS(file="T17_2_gblup_prediction_all_6001_7297.rds") +T17_2_gblup_prediction_all=c(T17_2_gblup_prediction_all_1_1000,T17_2_gblup_prediction_all_1001_2000,T17_2_gblup_prediction_all_2001_3000,T17_2_gblup_prediction_all_3001_4000,T17_2_gblup_prediction_all_4001_5000,T17_2_gblup_prediction_all_5001_6000,T17_2_gblup_prediction_all_6001_7297) + +T17_2_gblup_variances_all_1_1000=readRDS(file="T17_2_gblup_variances_all_1_1000.rds") +T17_2_gblup_variances_all_1001_2000=readRDS(file="T17_2_gblup_variances_all_1001_2000.rds") +T17_2_gblup_variances_all_2001_3000=readRDS(file="T17_2_gblup_variances_all_2001_3000.rds") +T17_2_gblup_variances_all_3001_4000=readRDS(file="T17_2_gblup_variances_all_3001_4000.rds") +T17_2_gblup_variances_all_4001_5000=readRDS(file="T17_2_gblup_variances_all_4001_5000.rds") +T17_2_gblup_variances_all_5001_6000=readRDS(file="T17_2_gblup_variances_all_5001_6000.rds") +T17_2_gblup_variances_all_6001_7297=readRDS(file="T17_2_gblup_variances_all_6001_7297.rds") +T17_2_gblup_variances_all=c(T17_2_gblup_variances_all_1_1000,T17_2_gblup_variances_all_1001_2000,T17_2_gblup_variances_all_2001_3000,T17_2_gblup_variances_all_3001_4000,T17_2_gblup_variances_all_4001_5000,T17_2_gblup_variances_all_5001_6000,T17_2_gblup_variances_all_6001_7297) + +saveRDS(T17_2_gblup_prediction_all,"T17_2_gblup_prediction_all.rds") +saveRDS(T17_2_gblup_variances_all,"T17_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_2_gfblup_prediction_all_1_1000=readRDS(file="T17_2_gfblup_prediction_all_1_1000.rds") +T17_2_gfblup_prediction_all_1001_2000=readRDS(file="T17_2_gfblup_prediction_all_1001_2000.rds") +T17_2_gfblup_prediction_all_2001_3000=readRDS(file="T17_2_gfblup_prediction_all_2001_3000.rds") +T17_2_gfblup_prediction_all_3001_4000=readRDS(file="T17_2_gfblup_prediction_all_3001_4000.rds") +T17_2_gfblup_prediction_all_4001_5000=readRDS(file="T17_2_gfblup_prediction_all_4001_5000.rds") +T17_2_gfblup_prediction_all_5001_6000=readRDS(file="T17_2_gfblup_prediction_all_5001_6000.rds") +T17_2_gfblup_prediction_all_6001_7297=readRDS(file="T17_2_gfblup_prediction_all_6001_7297.rds") + +T17_2_gfblup_variances_all_1_1000=readRDS(file="T17_2_gfblup_variances_all_1_1000.rds") +T17_2_gfblup_variances_all_1001_2000=readRDS(file="T17_2_gfblup_variances_all_1001_2000.rds") +T17_2_gfblup_variances_all_2001_3000=readRDS(file="T17_2_gfblup_variances_all_2001_3000.rds") +T17_2_gfblup_variances_all_3001_4000=readRDS(file="T17_2_gfblup_variances_all_3001_4000.rds") +T17_2_gfblup_variances_all_4001_5000=readRDS(file="T17_2_gfblup_variances_all_4001_5000.rds") +T17_2_gfblup_variances_all_5001_6000=readRDS(file="T17_2_gfblup_variances_all_5001_6000.rds") +T17_2_gfblup_variances_all_6001_7297=readRDS(file="T17_2_gfblup_variances_all_6001_7297.rds") + +cycles=length(T17_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T17_2_gfblup_variances_all=rep(list(list()),cycles) +T17_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_1_1000[[r]]) + T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_1001_2000[[r]]) + T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_2001_3000[[r]]) + T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_3001_4000[[r]]) + T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_4001_5000[[r]]) + T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_5001_6000[[r]]) + T17_2_gfblup_prediction_all[[r]]<-c(T17_2_gfblup_prediction_all[[r]],T17_2_gfblup_prediction_all_6001_7297[[r]]) + + T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_1_1000[[r]]) + T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_1001_2000[[r]]) + T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_2001_3000[[r]]) + T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_3001_4000[[r]]) + T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_4001_5000[[r]]) + T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_5001_6000[[r]]) + T17_2_gfblup_variances_all[[r]]<-c(T17_2_gfblup_variances_all[[r]],T17_2_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T17_2_gfblup_prediction_all,"T17_2_gfblup_prediction_all.rds") +saveRDS(T17_2_gfblup_variances_all,"T17_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_3_gblup_prediction_all_1_1000=readRDS(file="T17_3_gblup_prediction_all_1_1000.rds") +T17_3_gblup_prediction_all_1001_2000=readRDS(file="T17_3_gblup_prediction_all_1001_2000.rds") +T17_3_gblup_prediction_all_2001_3000=readRDS(file="T17_3_gblup_prediction_all_2001_3000.rds") +T17_3_gblup_prediction_all_3001_4000=readRDS(file="T17_3_gblup_prediction_all_3001_4000.rds") +T17_3_gblup_prediction_all_4001_5000=readRDS(file="T17_3_gblup_prediction_all_4001_5000.rds") +T17_3_gblup_prediction_all_5001_6000=readRDS(file="T17_3_gblup_prediction_all_5001_6000.rds") +T17_3_gblup_prediction_all_6001_7297=readRDS(file="T17_3_gblup_prediction_all_6001_7297.rds") +T17_3_gblup_prediction_all=c(T17_3_gblup_prediction_all_1_1000,T17_3_gblup_prediction_all_1001_2000,T17_3_gblup_prediction_all_2001_3000,T17_3_gblup_prediction_all_3001_4000,T17_3_gblup_prediction_all_4001_5000,T17_3_gblup_prediction_all_5001_6000,T17_3_gblup_prediction_all_6001_7297) + +T17_3_gblup_variances_all_1_1000=readRDS(file="T17_3_gblup_variances_all_1_1000.rds") +T17_3_gblup_variances_all_1001_2000=readRDS(file="T17_3_gblup_variances_all_1001_2000.rds") +T17_3_gblup_variances_all_2001_3000=readRDS(file="T17_3_gblup_variances_all_2001_3000.rds") +T17_3_gblup_variances_all_3001_4000=readRDS(file="T17_3_gblup_variances_all_3001_4000.rds") +T17_3_gblup_variances_all_4001_5000=readRDS(file="T17_3_gblup_variances_all_4001_5000.rds") +T17_3_gblup_variances_all_5001_6000=readRDS(file="T17_3_gblup_variances_all_5001_6000.rds") +T17_3_gblup_variances_all_6001_7297=readRDS(file="T17_3_gblup_variances_all_6001_7297.rds") +T17_3_gblup_variances_all=c(T17_3_gblup_variances_all_1_1000,T17_3_gblup_variances_all_1001_2000,T17_3_gblup_variances_all_2001_3000,T17_3_gblup_variances_all_3001_4000,T17_3_gblup_variances_all_4001_5000,T17_3_gblup_variances_all_5001_6000,T17_3_gblup_variances_all_6001_7297) + +saveRDS(T17_3_gblup_prediction_all,"T17_3_gblup_prediction_all.rds") +saveRDS(T17_3_gblup_variances_all,"T17_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_3_gfblup_prediction_all_1_1000=readRDS(file="T17_3_gfblup_prediction_all_1_1000.rds") +T17_3_gfblup_prediction_all_1001_2000=readRDS(file="T17_3_gfblup_prediction_all_1001_2000.rds") +T17_3_gfblup_prediction_all_2001_3000=readRDS(file="T17_3_gfblup_prediction_all_2001_3000.rds") +T17_3_gfblup_prediction_all_3001_4000=readRDS(file="T17_3_gfblup_prediction_all_3001_4000.rds") +T17_3_gfblup_prediction_all_4001_5000=readRDS(file="T17_3_gfblup_prediction_all_4001_5000.rds") +T17_3_gfblup_prediction_all_5001_6000=readRDS(file="T17_3_gfblup_prediction_all_5001_6000.rds") +T17_3_gfblup_prediction_all_6001_7297=readRDS(file="T17_3_gfblup_prediction_all_6001_7297.rds") + +T17_3_gfblup_variances_all_1_1000=readRDS(file="T17_3_gfblup_variances_all_1_1000.rds") +T17_3_gfblup_variances_all_1001_2000=readRDS(file="T17_3_gfblup_variances_all_1001_2000.rds") +T17_3_gfblup_variances_all_2001_3000=readRDS(file="T17_3_gfblup_variances_all_2001_3000.rds") +T17_3_gfblup_variances_all_3001_4000=readRDS(file="T17_3_gfblup_variances_all_3001_4000.rds") +T17_3_gfblup_variances_all_4001_5000=readRDS(file="T17_3_gfblup_variances_all_4001_5000.rds") +T17_3_gfblup_variances_all_5001_6000=readRDS(file="T17_3_gfblup_variances_all_5001_6000.rds") +T17_3_gfblup_variances_all_6001_7297=readRDS(file="T17_3_gfblup_variances_all_6001_7297.rds") + +cycles=length(T17_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T17_3_gfblup_variances_all=rep(list(list()),cycles) +T17_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_1_1000[[r]]) + T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_1001_2000[[r]]) + T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_2001_3000[[r]]) + T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_3001_4000[[r]]) + T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_4001_5000[[r]]) + T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_5001_6000[[r]]) + T17_3_gfblup_prediction_all[[r]]<-c(T17_3_gfblup_prediction_all[[r]],T17_3_gfblup_prediction_all_6001_7297[[r]]) + + T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_1_1000[[r]]) + T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_1001_2000[[r]]) + T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_2001_3000[[r]]) + T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_3001_4000[[r]]) + T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_4001_5000[[r]]) + T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_5001_6000[[r]]) + T17_3_gfblup_variances_all[[r]]<-c(T17_3_gfblup_variances_all[[r]],T17_3_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T17_3_gfblup_prediction_all,"T17_3_gfblup_prediction_all.rds") +saveRDS(T17_3_gfblup_variances_all,"T17_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_4_gblup_prediction_all_1_1000=readRDS(file="T17_4_gblup_prediction_all_1_1000.rds") +T17_4_gblup_prediction_all_1001_2000=readRDS(file="T17_4_gblup_prediction_all_1001_2000.rds") +T17_4_gblup_prediction_all_2001_3000=readRDS(file="T17_4_gblup_prediction_all_2001_3000.rds") +T17_4_gblup_prediction_all_3001_4000=readRDS(file="T17_4_gblup_prediction_all_3001_4000.rds") +T17_4_gblup_prediction_all_4001_5000=readRDS(file="T17_4_gblup_prediction_all_4001_5000.rds") +T17_4_gblup_prediction_all_5001_6000=readRDS(file="T17_4_gblup_prediction_all_5001_6000.rds") +T17_4_gblup_prediction_all_6001_7297=readRDS(file="T17_4_gblup_prediction_all_6001_7297.rds") +T17_4_gblup_prediction_all=c(T17_4_gblup_prediction_all_1_1000,T17_4_gblup_prediction_all_1001_2000,T17_4_gblup_prediction_all_2001_3000,T17_4_gblup_prediction_all_3001_4000,T17_4_gblup_prediction_all_4001_5000,T17_4_gblup_prediction_all_5001_6000,T17_4_gblup_prediction_all_6001_7297) + +T17_4_gblup_variances_all_1_1000=readRDS(file="T17_4_gblup_variances_all_1_1000.rds") +T17_4_gblup_variances_all_1001_2000=readRDS(file="T17_4_gblup_variances_all_1001_2000.rds") +T17_4_gblup_variances_all_2001_3000=readRDS(file="T17_4_gblup_variances_all_2001_3000.rds") +T17_4_gblup_variances_all_3001_4000=readRDS(file="T17_4_gblup_variances_all_3001_4000.rds") +T17_4_gblup_variances_all_4001_5000=readRDS(file="T17_4_gblup_variances_all_4001_5000.rds") +T17_4_gblup_variances_all_5001_6000=readRDS(file="T17_4_gblup_variances_all_5001_6000.rds") +T17_4_gblup_variances_all_6001_7297=readRDS(file="T17_4_gblup_variances_all_6001_7297.rds") +T17_4_gblup_variances_all=c(T17_4_gblup_variances_all_1_1000,T17_4_gblup_variances_all_1001_2000,T17_4_gblup_variances_all_2001_3000,T17_4_gblup_variances_all_3001_4000,T17_4_gblup_variances_all_4001_5000,T17_4_gblup_variances_all_5001_6000,T17_4_gblup_variances_all_6001_7297) + +saveRDS(T17_4_gblup_prediction_all,"T17_4_gblup_prediction_all.rds") +saveRDS(T17_4_gblup_variances_all,"T17_4_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_4_gfblup_prediction_all_1_1000=readRDS(file="T17_4_gfblup_prediction_all_1_1000.rds") +T17_4_gfblup_prediction_all_1001_2000=readRDS(file="T17_4_gfblup_prediction_all_1001_2000.rds") +T17_4_gfblup_prediction_all_2001_3000=readRDS(file="T17_4_gfblup_prediction_all_2001_3000.rds") +T17_4_gfblup_prediction_all_3001_4000=readRDS(file="T17_4_gfblup_prediction_all_3001_4000.rds") +T17_4_gfblup_prediction_all_4001_5000=readRDS(file="T17_4_gfblup_prediction_all_4001_5000.rds") +T17_4_gfblup_prediction_all_5001_6000=readRDS(file="T17_4_gfblup_prediction_all_5001_6000.rds") +T17_4_gfblup_prediction_all_6001_7297=readRDS(file="T17_4_gfblup_prediction_all_6001_7297.rds") + +T17_4_gfblup_variances_all_1_1000=readRDS(file="T17_4_gfblup_variances_all_1_1000.rds") +T17_4_gfblup_variances_all_1001_2000=readRDS(file="T17_4_gfblup_variances_all_1001_2000.rds") +T17_4_gfblup_variances_all_2001_3000=readRDS(file="T17_4_gfblup_variances_all_2001_3000.rds") +T17_4_gfblup_variances_all_3001_4000=readRDS(file="T17_4_gfblup_variances_all_3001_4000.rds") +T17_4_gfblup_variances_all_4001_5000=readRDS(file="T17_4_gfblup_variances_all_4001_5000.rds") +T17_4_gfblup_variances_all_5001_6000=readRDS(file="T17_4_gfblup_variances_all_5001_6000.rds") +T17_4_gfblup_variances_all_6001_7297=readRDS(file="T17_4_gfblup_variances_all_6001_7297.rds") + +cycles=length(T17_4_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T17_4_gfblup_variances_all=rep(list(list()),cycles) +T17_4_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_1_1000[[r]]) + T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_1001_2000[[r]]) + T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_2001_3000[[r]]) + T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_3001_4000[[r]]) + T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_4001_5000[[r]]) + T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_5001_6000[[r]]) + T17_4_gfblup_prediction_all[[r]]<-c(T17_4_gfblup_prediction_all[[r]],T17_4_gfblup_prediction_all_6001_7297[[r]]) + + T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_1_1000[[r]]) + T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_1001_2000[[r]]) + T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_2001_3000[[r]]) + T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_3001_4000[[r]]) + T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_4001_5000[[r]]) + T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_5001_6000[[r]]) + T17_4_gfblup_variances_all[[r]]<-c(T17_4_gfblup_variances_all[[r]],T17_4_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T17_4_gfblup_prediction_all,"T17_4_gfblup_prediction_all.rds") +saveRDS(T17_4_gfblup_variances_all,"T17_4_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_5_gblup_prediction_all_1_1000=readRDS(file="T17_5_gblup_prediction_all_1_1000.rds") +T17_5_gblup_prediction_all_1001_2000=readRDS(file="T17_5_gblup_prediction_all_1001_2000.rds") +T17_5_gblup_prediction_all_2001_3000=readRDS(file="T17_5_gblup_prediction_all_2001_3000.rds") +T17_5_gblup_prediction_all_3001_4000=readRDS(file="T17_5_gblup_prediction_all_3001_4000.rds") +T17_5_gblup_prediction_all_4001_5000=readRDS(file="T17_5_gblup_prediction_all_4001_5000.rds") +T17_5_gblup_prediction_all_5001_6000=readRDS(file="T17_5_gblup_prediction_all_5001_6000.rds") +T17_5_gblup_prediction_all_6001_7297=readRDS(file="T17_5_gblup_prediction_all_6001_7297.rds") +T17_5_gblup_prediction_all=c(T17_5_gblup_prediction_all_1_1000,T17_5_gblup_prediction_all_1001_2000,T17_5_gblup_prediction_all_2001_3000,T17_5_gblup_prediction_all_3001_4000,T17_5_gblup_prediction_all_4001_5000,T17_5_gblup_prediction_all_5001_6000,T17_5_gblup_prediction_all_6001_7297) + +T17_5_gblup_variances_all_1_1000=readRDS(file="T17_5_gblup_variances_all_1_1000.rds") +T17_5_gblup_variances_all_1001_2000=readRDS(file="T17_5_gblup_variances_all_1001_2000.rds") +T17_5_gblup_variances_all_2001_3000=readRDS(file="T17_5_gblup_variances_all_2001_3000.rds") +T17_5_gblup_variances_all_3001_4000=readRDS(file="T17_5_gblup_variances_all_3001_4000.rds") +T17_5_gblup_variances_all_4001_5000=readRDS(file="T17_5_gblup_variances_all_4001_5000.rds") +T17_5_gblup_variances_all_5001_6000=readRDS(file="T17_5_gblup_variances_all_5001_6000.rds") +T17_5_gblup_variances_all_6001_7297=readRDS(file="T17_5_gblup_variances_all_6001_7297.rds") +T17_5_gblup_variances_all=c(T17_5_gblup_variances_all_1_1000,T17_5_gblup_variances_all_1001_2000,T17_5_gblup_variances_all_2001_3000,T17_5_gblup_variances_all_3001_4000,T17_5_gblup_variances_all_4001_5000,T17_5_gblup_variances_all_5001_6000,T17_5_gblup_variances_all_6001_7297) + +saveRDS(T17_5_gblup_prediction_all,"T17_5_gblup_prediction_all.rds") +saveRDS(T17_5_gblup_variances_all,"T17_5_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_5_gfblup_prediction_all_1_1000=readRDS(file="T17_5_gfblup_prediction_all_1_1000.rds") +T17_5_gfblup_prediction_all_1001_2000=readRDS(file="T17_5_gfblup_prediction_all_1001_2000.rds") +T17_5_gfblup_prediction_all_2001_3000=readRDS(file="T17_5_gfblup_prediction_all_2001_3000.rds") +T17_5_gfblup_prediction_all_3001_4000=readRDS(file="T17_5_gfblup_prediction_all_3001_4000.rds") +T17_5_gfblup_prediction_all_4001_5000=readRDS(file="T17_5_gfblup_prediction_all_4001_5000.rds") +T17_5_gfblup_prediction_all_5001_6000=readRDS(file="T17_5_gfblup_prediction_all_5001_6000.rds") +T17_5_gfblup_prediction_all_6001_7297=readRDS(file="T17_5_gfblup_prediction_all_6001_7297.rds") + +T17_5_gfblup_variances_all_1_1000=readRDS(file="T17_5_gfblup_variances_all_1_1000.rds") +T17_5_gfblup_variances_all_1001_2000=readRDS(file="T17_5_gfblup_variances_all_1001_2000.rds") +T17_5_gfblup_variances_all_2001_3000=readRDS(file="T17_5_gfblup_variances_all_2001_3000.rds") +T17_5_gfblup_variances_all_3001_4000=readRDS(file="T17_5_gfblup_variances_all_3001_4000.rds") +T17_5_gfblup_variances_all_4001_5000=readRDS(file="T17_5_gfblup_variances_all_4001_5000.rds") +T17_5_gfblup_variances_all_5001_6000=readRDS(file="T17_5_gfblup_variances_all_5001_6000.rds") +T17_5_gfblup_variances_all_6001_7297=readRDS(file="T17_5_gfblup_variances_all_6001_7297.rds") + +cycles=length(T17_5_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T17_5_gfblup_variances_all=rep(list(list()),cycles) +T17_5_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_1_1000[[r]]) + T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_1001_2000[[r]]) + T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_2001_3000[[r]]) + T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_3001_4000[[r]]) + T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_4001_5000[[r]]) + T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_5001_6000[[r]]) + T17_5_gfblup_prediction_all[[r]]<-c(T17_5_gfblup_prediction_all[[r]],T17_5_gfblup_prediction_all_6001_7297[[r]]) + + T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_1_1000[[r]]) + T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_1001_2000[[r]]) + T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_2001_3000[[r]]) + T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_3001_4000[[r]]) + T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_4001_5000[[r]]) + T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_5001_6000[[r]]) + T17_5_gfblup_variances_all[[r]]<-c(T17_5_gfblup_variances_all[[r]],T17_5_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T17_5_gfblup_prediction_all,"T17_5_gfblup_prediction_all.rds") +saveRDS(T17_5_gfblup_variances_all,"T17_5_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_6_gblup_prediction_all_1_1000=readRDS(file="T17_6_gblup_prediction_all_1_1000.rds") +T17_6_gblup_prediction_all_1001_2000=readRDS(file="T17_6_gblup_prediction_all_1001_2000.rds") +T17_6_gblup_prediction_all_2001_3000=readRDS(file="T17_6_gblup_prediction_all_2001_3000.rds") +T17_6_gblup_prediction_all_3001_4000=readRDS(file="T17_6_gblup_prediction_all_3001_4000.rds") +T17_6_gblup_prediction_all_4001_5000=readRDS(file="T17_6_gblup_prediction_all_4001_5000.rds") +T17_6_gblup_prediction_all_5001_6000=readRDS(file="T17_6_gblup_prediction_all_5001_6000.rds") +T17_6_gblup_prediction_all_6001_7297=readRDS(file="T17_6_gblup_prediction_all_6001_7297.rds") +T17_6_gblup_prediction_all=c(T17_6_gblup_prediction_all_1_1000,T17_6_gblup_prediction_all_1001_2000,T17_6_gblup_prediction_all_2001_3000,T17_6_gblup_prediction_all_3001_4000,T17_6_gblup_prediction_all_4001_5000,T17_6_gblup_prediction_all_5001_6000,T17_6_gblup_prediction_all_6001_7297) + +T17_6_gblup_variances_all_1_1000=readRDS(file="T17_6_gblup_variances_all_1_1000.rds") +T17_6_gblup_variances_all_1001_2000=readRDS(file="T17_6_gblup_variances_all_1001_2000.rds") +T17_6_gblup_variances_all_2001_3000=readRDS(file="T17_6_gblup_variances_all_2001_3000.rds") +T17_6_gblup_variances_all_3001_4000=readRDS(file="T17_6_gblup_variances_all_3001_4000.rds") +T17_6_gblup_variances_all_4001_5000=readRDS(file="T17_6_gblup_variances_all_4001_5000.rds") +T17_6_gblup_variances_all_5001_6000=readRDS(file="T17_6_gblup_variances_all_5001_6000.rds") +T17_6_gblup_variances_all_6001_7297=readRDS(file="T17_6_gblup_variances_all_6001_7297.rds") +T17_6_gblup_variances_all=c(T17_6_gblup_variances_all_1_1000,T17_6_gblup_variances_all_1001_2000,T17_6_gblup_variances_all_2001_3000,T17_6_gblup_variances_all_3001_4000,T17_6_gblup_variances_all_4001_5000,T17_6_gblup_variances_all_5001_6000,T17_6_gblup_variances_all_6001_7297) + +saveRDS(T17_6_gblup_prediction_all,"T17_6_gblup_prediction_all.rds") +saveRDS(T17_6_gblup_variances_all,"T17_6_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_6_gfblup_prediction_all_1_1000=readRDS(file="T17_6_gfblup_prediction_all_1_1000.rds") +T17_6_gfblup_prediction_all_1001_2000=readRDS(file="T17_6_gfblup_prediction_all_1001_2000.rds") +T17_6_gfblup_prediction_all_2001_3000=readRDS(file="T17_6_gfblup_prediction_all_2001_3000.rds") +T17_6_gfblup_prediction_all_3001_4000=readRDS(file="T17_6_gfblup_prediction_all_3001_4000.rds") +T17_6_gfblup_prediction_all_4001_5000=readRDS(file="T17_6_gfblup_prediction_all_4001_5000.rds") +T17_6_gfblup_prediction_all_5001_6000=readRDS(file="T17_6_gfblup_prediction_all_5001_6000.rds") +T17_6_gfblup_prediction_all_6001_7297=readRDS(file="T17_6_gfblup_prediction_all_6001_7297.rds") + +T17_6_gfblup_variances_all_1_1000=readRDS(file="T17_6_gfblup_variances_all_1_1000.rds") +T17_6_gfblup_variances_all_1001_2000=readRDS(file="T17_6_gfblup_variances_all_1001_2000.rds") +T17_6_gfblup_variances_all_2001_3000=readRDS(file="T17_6_gfblup_variances_all_2001_3000.rds") +T17_6_gfblup_variances_all_3001_4000=readRDS(file="T17_6_gfblup_variances_all_3001_4000.rds") +T17_6_gfblup_variances_all_4001_5000=readRDS(file="T17_6_gfblup_variances_all_4001_5000.rds") +T17_6_gfblup_variances_all_5001_6000=readRDS(file="T17_6_gfblup_variances_all_5001_6000.rds") +T17_6_gfblup_variances_all_6001_7297=readRDS(file="T17_6_gfblup_variances_all_6001_7297.rds") + +cycles=length(T17_6_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T17_6_gfblup_variances_all=rep(list(list()),cycles) +T17_6_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_1_1000[[r]]) + T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_1001_2000[[r]]) + T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_2001_3000[[r]]) + T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_3001_4000[[r]]) + T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_4001_5000[[r]]) + T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_5001_6000[[r]]) + T17_6_gfblup_prediction_all[[r]]<-c(T17_6_gfblup_prediction_all[[r]],T17_6_gfblup_prediction_all_6001_7297[[r]]) + + T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_1_1000[[r]]) + T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_1001_2000[[r]]) + T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_2001_3000[[r]]) + T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_3001_4000[[r]]) + T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_4001_5000[[r]]) + T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_5001_6000[[r]]) + T17_6_gfblup_variances_all[[r]]<-c(T17_6_gfblup_variances_all[[r]],T17_6_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T17_6_gfblup_prediction_all,"T17_6_gfblup_prediction_all.rds") +saveRDS(T17_6_gfblup_variances_all,"T17_6_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_7_gblup_prediction_all_1_1000=readRDS(file="T17_7_gblup_prediction_all_1_1000.rds") +T17_7_gblup_prediction_all_1001_2000=readRDS(file="T17_7_gblup_prediction_all_1001_2000.rds") +T17_7_gblup_prediction_all_2001_3000=readRDS(file="T17_7_gblup_prediction_all_2001_3000.rds") +T17_7_gblup_prediction_all_3001_4000=readRDS(file="T17_7_gblup_prediction_all_3001_4000.rds") +T17_7_gblup_prediction_all_4001_5000=readRDS(file="T17_7_gblup_prediction_all_4001_5000.rds") +T17_7_gblup_prediction_all_5001_6000=readRDS(file="T17_7_gblup_prediction_all_5001_6000.rds") +T17_7_gblup_prediction_all_6001_7297=readRDS(file="T17_7_gblup_prediction_all_6001_7297.rds") +T17_7_gblup_prediction_all=c(T17_7_gblup_prediction_all_1_1000,T17_7_gblup_prediction_all_1001_2000,T17_7_gblup_prediction_all_2001_3000,T17_7_gblup_prediction_all_3001_4000,T17_7_gblup_prediction_all_4001_5000,T17_7_gblup_prediction_all_5001_6000,T17_7_gblup_prediction_all_6001_7297) + +T17_7_gblup_variances_all_1_1000=readRDS(file="T17_7_gblup_variances_all_1_1000.rds") +T17_7_gblup_variances_all_1001_2000=readRDS(file="T17_7_gblup_variances_all_1001_2000.rds") +T17_7_gblup_variances_all_2001_3000=readRDS(file="T17_7_gblup_variances_all_2001_3000.rds") +T17_7_gblup_variances_all_3001_4000=readRDS(file="T17_7_gblup_variances_all_3001_4000.rds") +T17_7_gblup_variances_all_4001_5000=readRDS(file="T17_7_gblup_variances_all_4001_5000.rds") +T17_7_gblup_variances_all_5001_6000=readRDS(file="T17_7_gblup_variances_all_5001_6000.rds") +T17_7_gblup_variances_all_6001_7297=readRDS(file="T17_7_gblup_variances_all_6001_7297.rds") +T17_7_gblup_variances_all=c(T17_7_gblup_variances_all_1_1000,T17_7_gblup_variances_all_1001_2000,T17_7_gblup_variances_all_2001_3000,T17_7_gblup_variances_all_3001_4000,T17_7_gblup_variances_all_4001_5000,T17_7_gblup_variances_all_5001_6000,T17_7_gblup_variances_all_6001_7297) + +saveRDS(T17_7_gblup_prediction_all,"T17_7_gblup_prediction_all.rds") +saveRDS(T17_7_gblup_variances_all,"T17_7_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_7_gfblup_prediction_all_1_1000=readRDS(file="T17_7_gfblup_prediction_all_1_1000.rds") +T17_7_gfblup_prediction_all_1001_2000=readRDS(file="T17_7_gfblup_prediction_all_1001_2000.rds") +T17_7_gfblup_prediction_all_2001_3000=readRDS(file="T17_7_gfblup_prediction_all_2001_3000.rds") +T17_7_gfblup_prediction_all_3001_4000=readRDS(file="T17_7_gfblup_prediction_all_3001_4000.rds") +T17_7_gfblup_prediction_all_4001_5000=readRDS(file="T17_7_gfblup_prediction_all_4001_5000.rds") +T17_7_gfblup_prediction_all_5001_6000=readRDS(file="T17_7_gfblup_prediction_all_5001_6000.rds") +T17_7_gfblup_prediction_all_6001_7297=readRDS(file="T17_7_gfblup_prediction_all_6001_7297.rds") + +T17_7_gfblup_variances_all_1_1000=readRDS(file="T17_7_gfblup_variances_all_1_1000.rds") +T17_7_gfblup_variances_all_1001_2000=readRDS(file="T17_7_gfblup_variances_all_1001_2000.rds") +T17_7_gfblup_variances_all_2001_3000=readRDS(file="T17_7_gfblup_variances_all_2001_3000.rds") +T17_7_gfblup_variances_all_3001_4000=readRDS(file="T17_7_gfblup_variances_all_3001_4000.rds") +T17_7_gfblup_variances_all_4001_5000=readRDS(file="T17_7_gfblup_variances_all_4001_5000.rds") +T17_7_gfblup_variances_all_5001_6000=readRDS(file="T17_7_gfblup_variances_all_5001_6000.rds") +T17_7_gfblup_variances_all_6001_7297=readRDS(file="T17_7_gfblup_variances_all_6001_7297.rds") + +cycles=length(T17_7_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T17_7_gfblup_variances_all=rep(list(list()),cycles) +T17_7_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_1_1000[[r]]) + T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_1001_2000[[r]]) + T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_2001_3000[[r]]) + T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_3001_4000[[r]]) + T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_4001_5000[[r]]) + T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_5001_6000[[r]]) + T17_7_gfblup_prediction_all[[r]]<-c(T17_7_gfblup_prediction_all[[r]],T17_7_gfblup_prediction_all_6001_7297[[r]]) + + T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_1_1000[[r]]) + T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_1001_2000[[r]]) + T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_2001_3000[[r]]) + T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_3001_4000[[r]]) + T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_4001_5000[[r]]) + T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_5001_6000[[r]]) + T17_7_gfblup_variances_all[[r]]<-c(T17_7_gfblup_variances_all[[r]],T17_7_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T17_7_gfblup_prediction_all,"T17_7_gfblup_prediction_all.rds") +saveRDS(T17_7_gfblup_variances_all,"T17_7_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_8_gblup_prediction_all_1_1000=readRDS(file="T17_8_gblup_prediction_all_1_1000.rds") +T17_8_gblup_prediction_all_1001_2000=readRDS(file="T17_8_gblup_prediction_all_1001_2000.rds") +T17_8_gblup_prediction_all_2001_3000=readRDS(file="T17_8_gblup_prediction_all_2001_3000.rds") +T17_8_gblup_prediction_all_3001_4000=readRDS(file="T17_8_gblup_prediction_all_3001_4000.rds") +T17_8_gblup_prediction_all_4001_5000=readRDS(file="T17_8_gblup_prediction_all_4001_5000.rds") +T17_8_gblup_prediction_all_5001_6000=readRDS(file="T17_8_gblup_prediction_all_5001_6000.rds") +T17_8_gblup_prediction_all_6001_7297=readRDS(file="T17_8_gblup_prediction_all_6001_7297.rds") +T17_8_gblup_prediction_all=c(T17_8_gblup_prediction_all_1_1000,T17_8_gblup_prediction_all_1001_2000,T17_8_gblup_prediction_all_2001_3000,T17_8_gblup_prediction_all_3001_4000,T17_8_gblup_prediction_all_4001_5000,T17_8_gblup_prediction_all_5001_6000,T17_8_gblup_prediction_all_6001_7297) + +T17_8_gblup_variances_all_1_1000=readRDS(file="T17_8_gblup_variances_all_1_1000.rds") +T17_8_gblup_variances_all_1001_2000=readRDS(file="T17_8_gblup_variances_all_1001_2000.rds") +T17_8_gblup_variances_all_2001_3000=readRDS(file="T17_8_gblup_variances_all_2001_3000.rds") +T17_8_gblup_variances_all_3001_4000=readRDS(file="T17_8_gblup_variances_all_3001_4000.rds") +T17_8_gblup_variances_all_4001_5000=readRDS(file="T17_8_gblup_variances_all_4001_5000.rds") +T17_8_gblup_variances_all_5001_6000=readRDS(file="T17_8_gblup_variances_all_5001_6000.rds") +T17_8_gblup_variances_all_6001_7297=readRDS(file="T17_8_gblup_variances_all_6001_7297.rds") +T17_8_gblup_variances_all=c(T17_8_gblup_variances_all_1_1000,T17_8_gblup_variances_all_1001_2000,T17_8_gblup_variances_all_2001_3000,T17_8_gblup_variances_all_3001_4000,T17_8_gblup_variances_all_4001_5000,T17_8_gblup_variances_all_5001_6000,T17_8_gblup_variances_all_6001_7297) + +saveRDS(T17_8_gblup_prediction_all,"T17_8_gblup_prediction_all.rds") +saveRDS(T17_8_gblup_variances_all,"T17_8_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T17_8_gfblup_prediction_all_1_1000=readRDS(file="T17_8_gfblup_prediction_all_1_1000.rds") +T17_8_gfblup_prediction_all_1001_2000=readRDS(file="T17_8_gfblup_prediction_all_1001_2000.rds") +T17_8_gfblup_prediction_all_2001_3000=readRDS(file="T17_8_gfblup_prediction_all_2001_3000.rds") +T17_8_gfblup_prediction_all_3001_4000=readRDS(file="T17_8_gfblup_prediction_all_3001_4000.rds") +T17_8_gfblup_prediction_all_4001_5000=readRDS(file="T17_8_gfblup_prediction_all_4001_5000.rds") +T17_8_gfblup_prediction_all_5001_6000=readRDS(file="T17_8_gfblup_prediction_all_5001_6000.rds") +T17_8_gfblup_prediction_all_6001_7297=readRDS(file="T17_8_gfblup_prediction_all_6001_7297.rds") + +T17_8_gfblup_variances_all_1_1000=readRDS(file="T17_8_gfblup_variances_all_1_1000.rds") +T17_8_gfblup_variances_all_1001_2000=readRDS(file="T17_8_gfblup_variances_all_1001_2000.rds") +T17_8_gfblup_variances_all_2001_3000=readRDS(file="T17_8_gfblup_variances_all_2001_3000.rds") +T17_8_gfblup_variances_all_3001_4000=readRDS(file="T17_8_gfblup_variances_all_3001_4000.rds") +T17_8_gfblup_variances_all_4001_5000=readRDS(file="T17_8_gfblup_variances_all_4001_5000.rds") +T17_8_gfblup_variances_all_5001_6000=readRDS(file="T17_8_gfblup_variances_all_5001_6000.rds") +T17_8_gfblup_variances_all_6001_7297=readRDS(file="T17_8_gfblup_variances_all_6001_7297.rds") + +cycles=length(T17_8_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T17_8_gfblup_variances_all=rep(list(list()),cycles) +T17_8_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_1_1000[[r]]) + T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_1001_2000[[r]]) + T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_2001_3000[[r]]) + T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_3001_4000[[r]]) + T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_4001_5000[[r]]) + T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_5001_6000[[r]]) + T17_8_gfblup_prediction_all[[r]]<-c(T17_8_gfblup_prediction_all[[r]],T17_8_gfblup_prediction_all_6001_7297[[r]]) + + T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_1_1000[[r]]) + T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_1001_2000[[r]]) + T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_2001_3000[[r]]) + T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_3001_4000[[r]]) + T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_4001_5000[[r]]) + T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_5001_6000[[r]]) + T17_8_gfblup_variances_all[[r]]<-c(T17_8_gfblup_variances_all[[r]],T17_8_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T17_8_gfblup_prediction_all,"T17_8_gfblup_prediction_all.rds") +saveRDS(T17_8_gfblup_variances_all,"T17_8_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_1_gblup_prediction_all_1_1000=readRDS(file="T18_1_gblup_prediction_all_1_1000.rds") +T18_1_gblup_prediction_all_1001_2000=readRDS(file="T18_1_gblup_prediction_all_1001_2000.rds") +T18_1_gblup_prediction_all_2001_3000=readRDS(file="T18_1_gblup_prediction_all_2001_3000.rds") +T18_1_gblup_prediction_all_3001_4000=readRDS(file="T18_1_gblup_prediction_all_3001_4000.rds") +T18_1_gblup_prediction_all_4001_5000=readRDS(file="T18_1_gblup_prediction_all_4001_5000.rds") +T18_1_gblup_prediction_all_5001_6000=readRDS(file="T18_1_gblup_prediction_all_5001_6000.rds") +T18_1_gblup_prediction_all_6001_7297=readRDS(file="T18_1_gblup_prediction_all_6001_7297.rds") +T18_1_gblup_prediction_all=c(T18_1_gblup_prediction_all_1_1000,T18_1_gblup_prediction_all_1001_2000,T18_1_gblup_prediction_all_2001_3000,T18_1_gblup_prediction_all_3001_4000,T18_1_gblup_prediction_all_4001_5000,T18_1_gblup_prediction_all_5001_6000,T18_1_gblup_prediction_all_6001_7297) + +T18_1_gblup_variances_all_1_1000=readRDS(file="T18_1_gblup_variances_all_1_1000.rds") +T18_1_gblup_variances_all_1001_2000=readRDS(file="T18_1_gblup_variances_all_1001_2000.rds") +T18_1_gblup_variances_all_2001_3000=readRDS(file="T18_1_gblup_variances_all_2001_3000.rds") +T18_1_gblup_variances_all_3001_4000=readRDS(file="T18_1_gblup_variances_all_3001_4000.rds") +T18_1_gblup_variances_all_4001_5000=readRDS(file="T18_1_gblup_variances_all_4001_5000.rds") +T18_1_gblup_variances_all_5001_6000=readRDS(file="T18_1_gblup_variances_all_5001_6000.rds") +T18_1_gblup_variances_all_6001_7297=readRDS(file="T18_1_gblup_variances_all_6001_7297.rds") +T18_1_gblup_variances_all=c(T18_1_gblup_variances_all_1_1000,T18_1_gblup_variances_all_1001_2000,T18_1_gblup_variances_all_2001_3000,T18_1_gblup_variances_all_3001_4000,T18_1_gblup_variances_all_4001_5000,T18_1_gblup_variances_all_5001_6000,T18_1_gblup_variances_all_6001_7297) + +saveRDS(T18_1_gblup_prediction_all,"T18_1_gblup_prediction_all.rds") +saveRDS(T18_1_gblup_variances_all,"T18_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_1_gfblup_prediction_all_1_1000=readRDS(file="T18_1_gfblup_prediction_all_1_1000.rds") +T18_1_gfblup_prediction_all_1001_2000=readRDS(file="T18_1_gfblup_prediction_all_1001_2000.rds") +T18_1_gfblup_prediction_all_2001_3000=readRDS(file="T18_1_gfblup_prediction_all_2001_3000.rds") +T18_1_gfblup_prediction_all_3001_4000=readRDS(file="T18_1_gfblup_prediction_all_3001_4000.rds") +T18_1_gfblup_prediction_all_4001_5000=readRDS(file="T18_1_gfblup_prediction_all_4001_5000.rds") +T18_1_gfblup_prediction_all_5001_6000=readRDS(file="T18_1_gfblup_prediction_all_5001_6000.rds") +T18_1_gfblup_prediction_all_6001_7297=readRDS(file="T18_1_gfblup_prediction_all_6001_7297.rds") + +T18_1_gfblup_variances_all_1_1000=readRDS(file="T18_1_gfblup_variances_all_1_1000.rds") +T18_1_gfblup_variances_all_1001_2000=readRDS(file="T18_1_gfblup_variances_all_1001_2000.rds") +T18_1_gfblup_variances_all_2001_3000=readRDS(file="T18_1_gfblup_variances_all_2001_3000.rds") +T18_1_gfblup_variances_all_3001_4000=readRDS(file="T18_1_gfblup_variances_all_3001_4000.rds") +T18_1_gfblup_variances_all_4001_5000=readRDS(file="T18_1_gfblup_variances_all_4001_5000.rds") +T18_1_gfblup_variances_all_5001_6000=readRDS(file="T18_1_gfblup_variances_all_5001_6000.rds") +T18_1_gfblup_variances_all_6001_7297=readRDS(file="T18_1_gfblup_variances_all_6001_7297.rds") + +cycles=length(T18_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T18_1_gfblup_variances_all=rep(list(list()),cycles) +T18_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_1_1000[[r]]) + T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_1001_2000[[r]]) + T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_2001_3000[[r]]) + T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_3001_4000[[r]]) + T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_4001_5000[[r]]) + T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_5001_6000[[r]]) + T18_1_gfblup_prediction_all[[r]]<-c(T18_1_gfblup_prediction_all[[r]],T18_1_gfblup_prediction_all_6001_7297[[r]]) + + T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_1_1000[[r]]) + T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_1001_2000[[r]]) + T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_2001_3000[[r]]) + T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_3001_4000[[r]]) + T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_4001_5000[[r]]) + T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_5001_6000[[r]]) + T18_1_gfblup_variances_all[[r]]<-c(T18_1_gfblup_variances_all[[r]],T18_1_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T18_1_gfblup_prediction_all,"T18_1_gfblup_prediction_all.rds") +saveRDS(T18_1_gfblup_variances_all,"T18_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_2_gblup_prediction_all_1_1000=readRDS(file="T18_2_gblup_prediction_all_1_1000.rds") +T18_2_gblup_prediction_all_1001_2000=readRDS(file="T18_2_gblup_prediction_all_1001_2000.rds") +T18_2_gblup_prediction_all_2001_3000=readRDS(file="T18_2_gblup_prediction_all_2001_3000.rds") +T18_2_gblup_prediction_all_3001_4000=readRDS(file="T18_2_gblup_prediction_all_3001_4000.rds") +T18_2_gblup_prediction_all_4001_5000=readRDS(file="T18_2_gblup_prediction_all_4001_5000.rds") +T18_2_gblup_prediction_all_5001_6000=readRDS(file="T18_2_gblup_prediction_all_5001_6000.rds") +T18_2_gblup_prediction_all_6001_7297=readRDS(file="T18_2_gblup_prediction_all_6001_7297.rds") +T18_2_gblup_prediction_all=c(T18_2_gblup_prediction_all_1_1000,T18_2_gblup_prediction_all_1001_2000,T18_2_gblup_prediction_all_2001_3000,T18_2_gblup_prediction_all_3001_4000,T18_2_gblup_prediction_all_4001_5000,T18_2_gblup_prediction_all_5001_6000,T18_2_gblup_prediction_all_6001_7297) + +T18_2_gblup_variances_all_1_1000=readRDS(file="T18_2_gblup_variances_all_1_1000.rds") +T18_2_gblup_variances_all_1001_2000=readRDS(file="T18_2_gblup_variances_all_1001_2000.rds") +T18_2_gblup_variances_all_2001_3000=readRDS(file="T18_2_gblup_variances_all_2001_3000.rds") +T18_2_gblup_variances_all_3001_4000=readRDS(file="T18_2_gblup_variances_all_3001_4000.rds") +T18_2_gblup_variances_all_4001_5000=readRDS(file="T18_2_gblup_variances_all_4001_5000.rds") +T18_2_gblup_variances_all_5001_6000=readRDS(file="T18_2_gblup_variances_all_5001_6000.rds") +T18_2_gblup_variances_all_6001_7297=readRDS(file="T18_2_gblup_variances_all_6001_7297.rds") +T18_2_gblup_variances_all=c(T18_2_gblup_variances_all_1_1000,T18_2_gblup_variances_all_1001_2000,T18_2_gblup_variances_all_2001_3000,T18_2_gblup_variances_all_3001_4000,T18_2_gblup_variances_all_4001_5000,T18_2_gblup_variances_all_5001_6000,T18_2_gblup_variances_all_6001_7297) + +saveRDS(T18_2_gblup_prediction_all,"T18_2_gblup_prediction_all.rds") +saveRDS(T18_2_gblup_variances_all,"T18_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_2_gfblup_prediction_all_1_1000=readRDS(file="T18_2_gfblup_prediction_all_1_1000.rds") +T18_2_gfblup_prediction_all_1001_2000=readRDS(file="T18_2_gfblup_prediction_all_1001_2000.rds") +T18_2_gfblup_prediction_all_2001_3000=readRDS(file="T18_2_gfblup_prediction_all_2001_3000.rds") +T18_2_gfblup_prediction_all_3001_4000=readRDS(file="T18_2_gfblup_prediction_all_3001_4000.rds") +T18_2_gfblup_prediction_all_4001_5000=readRDS(file="T18_2_gfblup_prediction_all_4001_5000.rds") +T18_2_gfblup_prediction_all_5001_6000=readRDS(file="T18_2_gfblup_prediction_all_5001_6000.rds") +T18_2_gfblup_prediction_all_6001_7297=readRDS(file="T18_2_gfblup_prediction_all_6001_7297.rds") + +T18_2_gfblup_variances_all_1_1000=readRDS(file="T18_2_gfblup_variances_all_1_1000.rds") +T18_2_gfblup_variances_all_1001_2000=readRDS(file="T18_2_gfblup_variances_all_1001_2000.rds") +T18_2_gfblup_variances_all_2001_3000=readRDS(file="T18_2_gfblup_variances_all_2001_3000.rds") +T18_2_gfblup_variances_all_3001_4000=readRDS(file="T18_2_gfblup_variances_all_3001_4000.rds") +T18_2_gfblup_variances_all_4001_5000=readRDS(file="T18_2_gfblup_variances_all_4001_5000.rds") +T18_2_gfblup_variances_all_5001_6000=readRDS(file="T18_2_gfblup_variances_all_5001_6000.rds") +T18_2_gfblup_variances_all_6001_7297=readRDS(file="T18_2_gfblup_variances_all_6001_7297.rds") + +cycles=length(T18_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T18_2_gfblup_variances_all=rep(list(list()),cycles) +T18_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_1_1000[[r]]) + T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_1001_2000[[r]]) + T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_2001_3000[[r]]) + T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_3001_4000[[r]]) + T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_4001_5000[[r]]) + T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_5001_6000[[r]]) + T18_2_gfblup_prediction_all[[r]]<-c(T18_2_gfblup_prediction_all[[r]],T18_2_gfblup_prediction_all_6001_7297[[r]]) + + T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_1_1000[[r]]) + T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_1001_2000[[r]]) + T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_2001_3000[[r]]) + T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_3001_4000[[r]]) + T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_4001_5000[[r]]) + T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_5001_6000[[r]]) + T18_2_gfblup_variances_all[[r]]<-c(T18_2_gfblup_variances_all[[r]],T18_2_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T18_2_gfblup_prediction_all,"T18_2_gfblup_prediction_all.rds") +saveRDS(T18_2_gfblup_variances_all,"T18_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_3_gblup_prediction_all_1_1000=readRDS(file="T18_3_gblup_prediction_all_1_1000.rds") +T18_3_gblup_prediction_all_1001_2000=readRDS(file="T18_3_gblup_prediction_all_1001_2000.rds") +T18_3_gblup_prediction_all_2001_3000=readRDS(file="T18_3_gblup_prediction_all_2001_3000.rds") +T18_3_gblup_prediction_all_3001_4000=readRDS(file="T18_3_gblup_prediction_all_3001_4000.rds") +T18_3_gblup_prediction_all_4001_5000=readRDS(file="T18_3_gblup_prediction_all_4001_5000.rds") +T18_3_gblup_prediction_all_5001_6000=readRDS(file="T18_3_gblup_prediction_all_5001_6000.rds") +T18_3_gblup_prediction_all_6001_7297=readRDS(file="T18_3_gblup_prediction_all_6001_7297.rds") +T18_3_gblup_prediction_all=c(T18_3_gblup_prediction_all_1_1000,T18_3_gblup_prediction_all_1001_2000,T18_3_gblup_prediction_all_2001_3000,T18_3_gblup_prediction_all_3001_4000,T18_3_gblup_prediction_all_4001_5000,T18_3_gblup_prediction_all_5001_6000,T18_3_gblup_prediction_all_6001_7297) + +T18_3_gblup_variances_all_1_1000=readRDS(file="T18_3_gblup_variances_all_1_1000.rds") +T18_3_gblup_variances_all_1001_2000=readRDS(file="T18_3_gblup_variances_all_1001_2000.rds") +T18_3_gblup_variances_all_2001_3000=readRDS(file="T18_3_gblup_variances_all_2001_3000.rds") +T18_3_gblup_variances_all_3001_4000=readRDS(file="T18_3_gblup_variances_all_3001_4000.rds") +T18_3_gblup_variances_all_4001_5000=readRDS(file="T18_3_gblup_variances_all_4001_5000.rds") +T18_3_gblup_variances_all_5001_6000=readRDS(file="T18_3_gblup_variances_all_5001_6000.rds") +T18_3_gblup_variances_all_6001_7297=readRDS(file="T18_3_gblup_variances_all_6001_7297.rds") +T18_3_gblup_variances_all=c(T18_3_gblup_variances_all_1_1000,T18_3_gblup_variances_all_1001_2000,T18_3_gblup_variances_all_2001_3000,T18_3_gblup_variances_all_3001_4000,T18_3_gblup_variances_all_4001_5000,T18_3_gblup_variances_all_5001_6000,T18_3_gblup_variances_all_6001_7297) + +saveRDS(T18_3_gblup_prediction_all,"T18_3_gblup_prediction_all.rds") +saveRDS(T18_3_gblup_variances_all,"T18_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_3_gfblup_prediction_all_1_1000=readRDS(file="T18_3_gfblup_prediction_all_1_1000.rds") +T18_3_gfblup_prediction_all_1001_2000=readRDS(file="T18_3_gfblup_prediction_all_1001_2000.rds") +T18_3_gfblup_prediction_all_2001_3000=readRDS(file="T18_3_gfblup_prediction_all_2001_3000.rds") +T18_3_gfblup_prediction_all_3001_4000=readRDS(file="T18_3_gfblup_prediction_all_3001_4000.rds") +T18_3_gfblup_prediction_all_4001_5000=readRDS(file="T18_3_gfblup_prediction_all_4001_5000.rds") +T18_3_gfblup_prediction_all_5001_6000=readRDS(file="T18_3_gfblup_prediction_all_5001_6000.rds") +T18_3_gfblup_prediction_all_6001_7297=readRDS(file="T18_3_gfblup_prediction_all_6001_7297.rds") + +T18_3_gfblup_variances_all_1_1000=readRDS(file="T18_3_gfblup_variances_all_1_1000.rds") +T18_3_gfblup_variances_all_1001_2000=readRDS(file="T18_3_gfblup_variances_all_1001_2000.rds") +T18_3_gfblup_variances_all_2001_3000=readRDS(file="T18_3_gfblup_variances_all_2001_3000.rds") +T18_3_gfblup_variances_all_3001_4000=readRDS(file="T18_3_gfblup_variances_all_3001_4000.rds") +T18_3_gfblup_variances_all_4001_5000=readRDS(file="T18_3_gfblup_variances_all_4001_5000.rds") +T18_3_gfblup_variances_all_5001_6000=readRDS(file="T18_3_gfblup_variances_all_5001_6000.rds") +T18_3_gfblup_variances_all_6001_7297=readRDS(file="T18_3_gfblup_variances_all_6001_7297.rds") + +cycles=length(T18_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T18_3_gfblup_variances_all=rep(list(list()),cycles) +T18_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_1_1000[[r]]) + T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_1001_2000[[r]]) + T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_2001_3000[[r]]) + T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_3001_4000[[r]]) + T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_4001_5000[[r]]) + T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_5001_6000[[r]]) + T18_3_gfblup_prediction_all[[r]]<-c(T18_3_gfblup_prediction_all[[r]],T18_3_gfblup_prediction_all_6001_7297[[r]]) + + T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_1_1000[[r]]) + T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_1001_2000[[r]]) + T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_2001_3000[[r]]) + T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_3001_4000[[r]]) + T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_4001_5000[[r]]) + T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_5001_6000[[r]]) + T18_3_gfblup_variances_all[[r]]<-c(T18_3_gfblup_variances_all[[r]],T18_3_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T18_3_gfblup_prediction_all,"T18_3_gfblup_prediction_all.rds") +saveRDS(T18_3_gfblup_variances_all,"T18_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_4_gblup_prediction_all_1_1000=readRDS(file="T18_4_gblup_prediction_all_1_1000.rds") +T18_4_gblup_prediction_all_1001_2000=readRDS(file="T18_4_gblup_prediction_all_1001_2000.rds") +T18_4_gblup_prediction_all_2001_3000=readRDS(file="T18_4_gblup_prediction_all_2001_3000.rds") +T18_4_gblup_prediction_all_3001_4000=readRDS(file="T18_4_gblup_prediction_all_3001_4000.rds") +T18_4_gblup_prediction_all_4001_5000=readRDS(file="T18_4_gblup_prediction_all_4001_5000.rds") +T18_4_gblup_prediction_all_5001_6000=readRDS(file="T18_4_gblup_prediction_all_5001_6000.rds") +T18_4_gblup_prediction_all_6001_7297=readRDS(file="T18_4_gblup_prediction_all_6001_7297.rds") +T18_4_gblup_prediction_all=c(T18_4_gblup_prediction_all_1_1000,T18_4_gblup_prediction_all_1001_2000,T18_4_gblup_prediction_all_2001_3000,T18_4_gblup_prediction_all_3001_4000,T18_4_gblup_prediction_all_4001_5000,T18_4_gblup_prediction_all_5001_6000,T18_4_gblup_prediction_all_6001_7297) + +T18_4_gblup_variances_all_1_1000=readRDS(file="T18_4_gblup_variances_all_1_1000.rds") +T18_4_gblup_variances_all_1001_2000=readRDS(file="T18_4_gblup_variances_all_1001_2000.rds") +T18_4_gblup_variances_all_2001_3000=readRDS(file="T18_4_gblup_variances_all_2001_3000.rds") +T18_4_gblup_variances_all_3001_4000=readRDS(file="T18_4_gblup_variances_all_3001_4000.rds") +T18_4_gblup_variances_all_4001_5000=readRDS(file="T18_4_gblup_variances_all_4001_5000.rds") +T18_4_gblup_variances_all_5001_6000=readRDS(file="T18_4_gblup_variances_all_5001_6000.rds") +T18_4_gblup_variances_all_6001_7297=readRDS(file="T18_4_gblup_variances_all_6001_7297.rds") +T18_4_gblup_variances_all=c(T18_4_gblup_variances_all_1_1000,T18_4_gblup_variances_all_1001_2000,T18_4_gblup_variances_all_2001_3000,T18_4_gblup_variances_all_3001_4000,T18_4_gblup_variances_all_4001_5000,T18_4_gblup_variances_all_5001_6000,T18_4_gblup_variances_all_6001_7297) + +saveRDS(T18_4_gblup_prediction_all,"T18_4_gblup_prediction_all.rds") +saveRDS(T18_4_gblup_variances_all,"T18_4_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_4_gfblup_prediction_all_1_1000=readRDS(file="T18_4_gfblup_prediction_all_1_1000.rds") +T18_4_gfblup_prediction_all_1001_2000=readRDS(file="T18_4_gfblup_prediction_all_1001_2000.rds") +T18_4_gfblup_prediction_all_2001_3000=readRDS(file="T18_4_gfblup_prediction_all_2001_3000.rds") +T18_4_gfblup_prediction_all_3001_4000=readRDS(file="T18_4_gfblup_prediction_all_3001_4000.rds") +T18_4_gfblup_prediction_all_4001_5000=readRDS(file="T18_4_gfblup_prediction_all_4001_5000.rds") +T18_4_gfblup_prediction_all_5001_6000=readRDS(file="T18_4_gfblup_prediction_all_5001_6000.rds") +T18_4_gfblup_prediction_all_6001_7297=readRDS(file="T18_4_gfblup_prediction_all_6001_7297.rds") + +T18_4_gfblup_variances_all_1_1000=readRDS(file="T18_4_gfblup_variances_all_1_1000.rds") +T18_4_gfblup_variances_all_1001_2000=readRDS(file="T18_4_gfblup_variances_all_1001_2000.rds") +T18_4_gfblup_variances_all_2001_3000=readRDS(file="T18_4_gfblup_variances_all_2001_3000.rds") +T18_4_gfblup_variances_all_3001_4000=readRDS(file="T18_4_gfblup_variances_all_3001_4000.rds") +T18_4_gfblup_variances_all_4001_5000=readRDS(file="T18_4_gfblup_variances_all_4001_5000.rds") +T18_4_gfblup_variances_all_5001_6000=readRDS(file="T18_4_gfblup_variances_all_5001_6000.rds") +T18_4_gfblup_variances_all_6001_7297=readRDS(file="T18_4_gfblup_variances_all_6001_7297.rds") + +cycles=length(T18_4_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T18_4_gfblup_variances_all=rep(list(list()),cycles) +T18_4_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_1_1000[[r]]) + T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_1001_2000[[r]]) + T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_2001_3000[[r]]) + T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_3001_4000[[r]]) + T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_4001_5000[[r]]) + T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_5001_6000[[r]]) + T18_4_gfblup_prediction_all[[r]]<-c(T18_4_gfblup_prediction_all[[r]],T18_4_gfblup_prediction_all_6001_7297[[r]]) + + T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_1_1000[[r]]) + T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_1001_2000[[r]]) + T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_2001_3000[[r]]) + T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_3001_4000[[r]]) + T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_4001_5000[[r]]) + T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_5001_6000[[r]]) + T18_4_gfblup_variances_all[[r]]<-c(T18_4_gfblup_variances_all[[r]],T18_4_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T18_4_gfblup_prediction_all,"T18_4_gfblup_prediction_all.rds") +saveRDS(T18_4_gfblup_variances_all,"T18_4_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_5_gblup_prediction_all_1_1000=readRDS(file="T18_5_gblup_prediction_all_1_1000.rds") +T18_5_gblup_prediction_all_1001_2000=readRDS(file="T18_5_gblup_prediction_all_1001_2000.rds") +T18_5_gblup_prediction_all_2001_3000=readRDS(file="T18_5_gblup_prediction_all_2001_3000.rds") +T18_5_gblup_prediction_all_3001_4000=readRDS(file="T18_5_gblup_prediction_all_3001_4000.rds") +T18_5_gblup_prediction_all_4001_5000=readRDS(file="T18_5_gblup_prediction_all_4001_5000.rds") +T18_5_gblup_prediction_all_5001_6000=readRDS(file="T18_5_gblup_prediction_all_5001_6000.rds") +T18_5_gblup_prediction_all_6001_7297=readRDS(file="T18_5_gblup_prediction_all_6001_7297.rds") +T18_5_gblup_prediction_all=c(T18_5_gblup_prediction_all_1_1000,T18_5_gblup_prediction_all_1001_2000,T18_5_gblup_prediction_all_2001_3000,T18_5_gblup_prediction_all_3001_4000,T18_5_gblup_prediction_all_4001_5000,T18_5_gblup_prediction_all_5001_6000,T18_5_gblup_prediction_all_6001_7297) + +T18_5_gblup_variances_all_1_1000=readRDS(file="T18_5_gblup_variances_all_1_1000.rds") +T18_5_gblup_variances_all_1001_2000=readRDS(file="T18_5_gblup_variances_all_1001_2000.rds") +T18_5_gblup_variances_all_2001_3000=readRDS(file="T18_5_gblup_variances_all_2001_3000.rds") +T18_5_gblup_variances_all_3001_4000=readRDS(file="T18_5_gblup_variances_all_3001_4000.rds") +T18_5_gblup_variances_all_4001_5000=readRDS(file="T18_5_gblup_variances_all_4001_5000.rds") +T18_5_gblup_variances_all_5001_6000=readRDS(file="T18_5_gblup_variances_all_5001_6000.rds") +T18_5_gblup_variances_all_6001_7297=readRDS(file="T18_5_gblup_variances_all_6001_7297.rds") +T18_5_gblup_variances_all=c(T18_5_gblup_variances_all_1_1000,T18_5_gblup_variances_all_1001_2000,T18_5_gblup_variances_all_2001_3000,T18_5_gblup_variances_all_3001_4000,T18_5_gblup_variances_all_4001_5000,T18_5_gblup_variances_all_5001_6000,T18_5_gblup_variances_all_6001_7297) + +saveRDS(T18_5_gblup_prediction_all,"T18_5_gblup_prediction_all.rds") +saveRDS(T18_5_gblup_variances_all,"T18_5_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_5_gfblup_prediction_all_1_1000=readRDS(file="T18_5_gfblup_prediction_all_1_1000.rds") +T18_5_gfblup_prediction_all_1001_2000=readRDS(file="T18_5_gfblup_prediction_all_1001_2000.rds") +T18_5_gfblup_prediction_all_2001_3000=readRDS(file="T18_5_gfblup_prediction_all_2001_3000.rds") +T18_5_gfblup_prediction_all_3001_4000=readRDS(file="T18_5_gfblup_prediction_all_3001_4000.rds") +T18_5_gfblup_prediction_all_4001_5000=readRDS(file="T18_5_gfblup_prediction_all_4001_5000.rds") +T18_5_gfblup_prediction_all_5001_6000=readRDS(file="T18_5_gfblup_prediction_all_5001_6000.rds") +T18_5_gfblup_prediction_all_6001_7297=readRDS(file="T18_5_gfblup_prediction_all_6001_7297.rds") + +T18_5_gfblup_variances_all_1_1000=readRDS(file="T18_5_gfblup_variances_all_1_1000.rds") +T18_5_gfblup_variances_all_1001_2000=readRDS(file="T18_5_gfblup_variances_all_1001_2000.rds") +T18_5_gfblup_variances_all_2001_3000=readRDS(file="T18_5_gfblup_variances_all_2001_3000.rds") +T18_5_gfblup_variances_all_3001_4000=readRDS(file="T18_5_gfblup_variances_all_3001_4000.rds") +T18_5_gfblup_variances_all_4001_5000=readRDS(file="T18_5_gfblup_variances_all_4001_5000.rds") +T18_5_gfblup_variances_all_5001_6000=readRDS(file="T18_5_gfblup_variances_all_5001_6000.rds") +T18_5_gfblup_variances_all_6001_7297=readRDS(file="T18_5_gfblup_variances_all_6001_7297.rds") + +cycles=length(T18_5_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T18_5_gfblup_variances_all=rep(list(list()),cycles) +T18_5_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_1_1000[[r]]) + T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_1001_2000[[r]]) + T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_2001_3000[[r]]) + T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_3001_4000[[r]]) + T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_4001_5000[[r]]) + T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_5001_6000[[r]]) + T18_5_gfblup_prediction_all[[r]]<-c(T18_5_gfblup_prediction_all[[r]],T18_5_gfblup_prediction_all_6001_7297[[r]]) + + T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_1_1000[[r]]) + T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_1001_2000[[r]]) + T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_2001_3000[[r]]) + T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_3001_4000[[r]]) + T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_4001_5000[[r]]) + T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_5001_6000[[r]]) + T18_5_gfblup_variances_all[[r]]<-c(T18_5_gfblup_variances_all[[r]],T18_5_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T18_5_gfblup_prediction_all,"T18_5_gfblup_prediction_all.rds") +saveRDS(T18_5_gfblup_variances_all,"T18_5_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_6_gblup_prediction_all_1_1000=readRDS(file="T18_6_gblup_prediction_all_1_1000.rds") +T18_6_gblup_prediction_all_1001_2000=readRDS(file="T18_6_gblup_prediction_all_1001_2000.rds") +T18_6_gblup_prediction_all_2001_3000=readRDS(file="T18_6_gblup_prediction_all_2001_3000.rds") +T18_6_gblup_prediction_all_3001_4000=readRDS(file="T18_6_gblup_prediction_all_3001_4000.rds") +T18_6_gblup_prediction_all_4001_5000=readRDS(file="T18_6_gblup_prediction_all_4001_5000.rds") +T18_6_gblup_prediction_all_5001_6000=readRDS(file="T18_6_gblup_prediction_all_5001_6000.rds") +T18_6_gblup_prediction_all_6001_7297=readRDS(file="T18_6_gblup_prediction_all_6001_7297.rds") +T18_6_gblup_prediction_all=c(T18_6_gblup_prediction_all_1_1000,T18_6_gblup_prediction_all_1001_2000,T18_6_gblup_prediction_all_2001_3000,T18_6_gblup_prediction_all_3001_4000,T18_6_gblup_prediction_all_4001_5000,T18_6_gblup_prediction_all_5001_6000,T18_6_gblup_prediction_all_6001_7297) + +T18_6_gblup_variances_all_1_1000=readRDS(file="T18_6_gblup_variances_all_1_1000.rds") +T18_6_gblup_variances_all_1001_2000=readRDS(file="T18_6_gblup_variances_all_1001_2000.rds") +T18_6_gblup_variances_all_2001_3000=readRDS(file="T18_6_gblup_variances_all_2001_3000.rds") +T18_6_gblup_variances_all_3001_4000=readRDS(file="T18_6_gblup_variances_all_3001_4000.rds") +T18_6_gblup_variances_all_4001_5000=readRDS(file="T18_6_gblup_variances_all_4001_5000.rds") +T18_6_gblup_variances_all_5001_6000=readRDS(file="T18_6_gblup_variances_all_5001_6000.rds") +T18_6_gblup_variances_all_6001_7297=readRDS(file="T18_6_gblup_variances_all_6001_7297.rds") +T18_6_gblup_variances_all=c(T18_6_gblup_variances_all_1_1000,T18_6_gblup_variances_all_1001_2000,T18_6_gblup_variances_all_2001_3000,T18_6_gblup_variances_all_3001_4000,T18_6_gblup_variances_all_4001_5000,T18_6_gblup_variances_all_5001_6000,T18_6_gblup_variances_all_6001_7297) + +saveRDS(T18_6_gblup_prediction_all,"T18_6_gblup_prediction_all.rds") +saveRDS(T18_6_gblup_variances_all,"T18_6_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_6_gfblup_prediction_all_1_1000=readRDS(file="T18_6_gfblup_prediction_all_1_1000.rds") +T18_6_gfblup_prediction_all_1001_2000=readRDS(file="T18_6_gfblup_prediction_all_1001_2000.rds") +T18_6_gfblup_prediction_all_2001_3000=readRDS(file="T18_6_gfblup_prediction_all_2001_3000.rds") +T18_6_gfblup_prediction_all_3001_4000=readRDS(file="T18_6_gfblup_prediction_all_3001_4000.rds") +T18_6_gfblup_prediction_all_4001_5000=readRDS(file="T18_6_gfblup_prediction_all_4001_5000.rds") +T18_6_gfblup_prediction_all_5001_6000=readRDS(file="T18_6_gfblup_prediction_all_5001_6000.rds") +T18_6_gfblup_prediction_all_6001_7297=readRDS(file="T18_6_gfblup_prediction_all_6001_7297.rds") + +T18_6_gfblup_variances_all_1_1000=readRDS(file="T18_6_gfblup_variances_all_1_1000.rds") +T18_6_gfblup_variances_all_1001_2000=readRDS(file="T18_6_gfblup_variances_all_1001_2000.rds") +T18_6_gfblup_variances_all_2001_3000=readRDS(file="T18_6_gfblup_variances_all_2001_3000.rds") +T18_6_gfblup_variances_all_3001_4000=readRDS(file="T18_6_gfblup_variances_all_3001_4000.rds") +T18_6_gfblup_variances_all_4001_5000=readRDS(file="T18_6_gfblup_variances_all_4001_5000.rds") +T18_6_gfblup_variances_all_5001_6000=readRDS(file="T18_6_gfblup_variances_all_5001_6000.rds") +T18_6_gfblup_variances_all_6001_7297=readRDS(file="T18_6_gfblup_variances_all_6001_7297.rds") + +cycles=length(T18_6_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T18_6_gfblup_variances_all=rep(list(list()),cycles) +T18_6_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_1_1000[[r]]) + T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_1001_2000[[r]]) + T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_2001_3000[[r]]) + T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_3001_4000[[r]]) + T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_4001_5000[[r]]) + T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_5001_6000[[r]]) + T18_6_gfblup_prediction_all[[r]]<-c(T18_6_gfblup_prediction_all[[r]],T18_6_gfblup_prediction_all_6001_7297[[r]]) + + T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_1_1000[[r]]) + T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_1001_2000[[r]]) + T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_2001_3000[[r]]) + T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_3001_4000[[r]]) + T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_4001_5000[[r]]) + T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_5001_6000[[r]]) + T18_6_gfblup_variances_all[[r]]<-c(T18_6_gfblup_variances_all[[r]],T18_6_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T18_6_gfblup_prediction_all,"T18_6_gfblup_prediction_all.rds") +saveRDS(T18_6_gfblup_variances_all,"T18_6_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_7_gblup_prediction_all_1_1000=readRDS(file="T18_7_gblup_prediction_all_1_1000.rds") +T18_7_gblup_prediction_all_1001_2000=readRDS(file="T18_7_gblup_prediction_all_1001_2000.rds") +T18_7_gblup_prediction_all_2001_3000=readRDS(file="T18_7_gblup_prediction_all_2001_3000.rds") +T18_7_gblup_prediction_all_3001_4000=readRDS(file="T18_7_gblup_prediction_all_3001_4000.rds") +T18_7_gblup_prediction_all_4001_5000=readRDS(file="T18_7_gblup_prediction_all_4001_5000.rds") +T18_7_gblup_prediction_all_5001_6000=readRDS(file="T18_7_gblup_prediction_all_5001_6000.rds") +T18_7_gblup_prediction_all_6001_7297=readRDS(file="T18_7_gblup_prediction_all_6001_7297.rds") +T18_7_gblup_prediction_all=c(T18_7_gblup_prediction_all_1_1000,T18_7_gblup_prediction_all_1001_2000,T18_7_gblup_prediction_all_2001_3000,T18_7_gblup_prediction_all_3001_4000,T18_7_gblup_prediction_all_4001_5000,T18_7_gblup_prediction_all_5001_6000,T18_7_gblup_prediction_all_6001_7297) + +T18_7_gblup_variances_all_1_1000=readRDS(file="T18_7_gblup_variances_all_1_1000.rds") +T18_7_gblup_variances_all_1001_2000=readRDS(file="T18_7_gblup_variances_all_1001_2000.rds") +T18_7_gblup_variances_all_2001_3000=readRDS(file="T18_7_gblup_variances_all_2001_3000.rds") +T18_7_gblup_variances_all_3001_4000=readRDS(file="T18_7_gblup_variances_all_3001_4000.rds") +T18_7_gblup_variances_all_4001_5000=readRDS(file="T18_7_gblup_variances_all_4001_5000.rds") +T18_7_gblup_variances_all_5001_6000=readRDS(file="T18_7_gblup_variances_all_5001_6000.rds") +T18_7_gblup_variances_all_6001_7297=readRDS(file="T18_7_gblup_variances_all_6001_7297.rds") +T18_7_gblup_variances_all=c(T18_7_gblup_variances_all_1_1000,T18_7_gblup_variances_all_1001_2000,T18_7_gblup_variances_all_2001_3000,T18_7_gblup_variances_all_3001_4000,T18_7_gblup_variances_all_4001_5000,T18_7_gblup_variances_all_5001_6000,T18_7_gblup_variances_all_6001_7297) + +saveRDS(T18_7_gblup_prediction_all,"T18_7_gblup_prediction_all.rds") +saveRDS(T18_7_gblup_variances_all,"T18_7_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_7_gfblup_prediction_all_1_1000=readRDS(file="T18_7_gfblup_prediction_all_1_1000.rds") +T18_7_gfblup_prediction_all_1001_2000=readRDS(file="T18_7_gfblup_prediction_all_1001_2000.rds") +T18_7_gfblup_prediction_all_2001_3000=readRDS(file="T18_7_gfblup_prediction_all_2001_3000.rds") +T18_7_gfblup_prediction_all_3001_4000=readRDS(file="T18_7_gfblup_prediction_all_3001_4000.rds") +T18_7_gfblup_prediction_all_4001_5000=readRDS(file="T18_7_gfblup_prediction_all_4001_5000.rds") +T18_7_gfblup_prediction_all_5001_6000=readRDS(file="T18_7_gfblup_prediction_all_5001_6000.rds") +T18_7_gfblup_prediction_all_6001_7297=readRDS(file="T18_7_gfblup_prediction_all_6001_7297.rds") + +T18_7_gfblup_variances_all_1_1000=readRDS(file="T18_7_gfblup_variances_all_1_1000.rds") +T18_7_gfblup_variances_all_1001_2000=readRDS(file="T18_7_gfblup_variances_all_1001_2000.rds") +T18_7_gfblup_variances_all_2001_3000=readRDS(file="T18_7_gfblup_variances_all_2001_3000.rds") +T18_7_gfblup_variances_all_3001_4000=readRDS(file="T18_7_gfblup_variances_all_3001_4000.rds") +T18_7_gfblup_variances_all_4001_5000=readRDS(file="T18_7_gfblup_variances_all_4001_5000.rds") +T18_7_gfblup_variances_all_5001_6000=readRDS(file="T18_7_gfblup_variances_all_5001_6000.rds") +T18_7_gfblup_variances_all_6001_7297=readRDS(file="T18_7_gfblup_variances_all_6001_7297.rds") + +cycles=length(T18_7_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T18_7_gfblup_variances_all=rep(list(list()),cycles) +T18_7_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_1_1000[[r]]) + T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_1001_2000[[r]]) + T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_2001_3000[[r]]) + T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_3001_4000[[r]]) + T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_4001_5000[[r]]) + T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_5001_6000[[r]]) + T18_7_gfblup_prediction_all[[r]]<-c(T18_7_gfblup_prediction_all[[r]],T18_7_gfblup_prediction_all_6001_7297[[r]]) + + T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_1_1000[[r]]) + T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_1001_2000[[r]]) + T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_2001_3000[[r]]) + T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_3001_4000[[r]]) + T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_4001_5000[[r]]) + T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_5001_6000[[r]]) + T18_7_gfblup_variances_all[[r]]<-c(T18_7_gfblup_variances_all[[r]],T18_7_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T18_7_gfblup_prediction_all,"T18_7_gfblup_prediction_all.rds") +saveRDS(T18_7_gfblup_variances_all,"T18_7_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_8_gblup_prediction_all_1_1000=readRDS(file="T18_8_gblup_prediction_all_1_1000.rds") +T18_8_gblup_prediction_all_1001_2000=readRDS(file="T18_8_gblup_prediction_all_1001_2000.rds") +T18_8_gblup_prediction_all_2001_3000=readRDS(file="T18_8_gblup_prediction_all_2001_3000.rds") +T18_8_gblup_prediction_all_3001_4000=readRDS(file="T18_8_gblup_prediction_all_3001_4000.rds") +T18_8_gblup_prediction_all_4001_5000=readRDS(file="T18_8_gblup_prediction_all_4001_5000.rds") +T18_8_gblup_prediction_all_5001_6000=readRDS(file="T18_8_gblup_prediction_all_5001_6000.rds") +T18_8_gblup_prediction_all_6001_7297=readRDS(file="T18_8_gblup_prediction_all_6001_7297.rds") +T18_8_gblup_prediction_all=c(T18_8_gblup_prediction_all_1_1000,T18_8_gblup_prediction_all_1001_2000,T18_8_gblup_prediction_all_2001_3000,T18_8_gblup_prediction_all_3001_4000,T18_8_gblup_prediction_all_4001_5000,T18_8_gblup_prediction_all_5001_6000,T18_8_gblup_prediction_all_6001_7297) + +T18_8_gblup_variances_all_1_1000=readRDS(file="T18_8_gblup_variances_all_1_1000.rds") +T18_8_gblup_variances_all_1001_2000=readRDS(file="T18_8_gblup_variances_all_1001_2000.rds") +T18_8_gblup_variances_all_2001_3000=readRDS(file="T18_8_gblup_variances_all_2001_3000.rds") +T18_8_gblup_variances_all_3001_4000=readRDS(file="T18_8_gblup_variances_all_3001_4000.rds") +T18_8_gblup_variances_all_4001_5000=readRDS(file="T18_8_gblup_variances_all_4001_5000.rds") +T18_8_gblup_variances_all_5001_6000=readRDS(file="T18_8_gblup_variances_all_5001_6000.rds") +T18_8_gblup_variances_all_6001_7297=readRDS(file="T18_8_gblup_variances_all_6001_7297.rds") +T18_8_gblup_variances_all=c(T18_8_gblup_variances_all_1_1000,T18_8_gblup_variances_all_1001_2000,T18_8_gblup_variances_all_2001_3000,T18_8_gblup_variances_all_3001_4000,T18_8_gblup_variances_all_4001_5000,T18_8_gblup_variances_all_5001_6000,T18_8_gblup_variances_all_6001_7297) + +saveRDS(T18_8_gblup_prediction_all,"T18_8_gblup_prediction_all.rds") +saveRDS(T18_8_gblup_variances_all,"T18_8_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T18_8_gfblup_prediction_all_1_1000=readRDS(file="T18_8_gfblup_prediction_all_1_1000.rds") +T18_8_gfblup_prediction_all_1001_2000=readRDS(file="T18_8_gfblup_prediction_all_1001_2000.rds") +T18_8_gfblup_prediction_all_2001_3000=readRDS(file="T18_8_gfblup_prediction_all_2001_3000.rds") +T18_8_gfblup_prediction_all_3001_4000=readRDS(file="T18_8_gfblup_prediction_all_3001_4000.rds") +T18_8_gfblup_prediction_all_4001_5000=readRDS(file="T18_8_gfblup_prediction_all_4001_5000.rds") +T18_8_gfblup_prediction_all_5001_6000=readRDS(file="T18_8_gfblup_prediction_all_5001_6000.rds") +T18_8_gfblup_prediction_all_6001_7297=readRDS(file="T18_8_gfblup_prediction_all_6001_7297.rds") + +T18_8_gfblup_variances_all_1_1000=readRDS(file="T18_8_gfblup_variances_all_1_1000.rds") +T18_8_gfblup_variances_all_1001_2000=readRDS(file="T18_8_gfblup_variances_all_1001_2000.rds") +T18_8_gfblup_variances_all_2001_3000=readRDS(file="T18_8_gfblup_variances_all_2001_3000.rds") +T18_8_gfblup_variances_all_3001_4000=readRDS(file="T18_8_gfblup_variances_all_3001_4000.rds") +T18_8_gfblup_variances_all_4001_5000=readRDS(file="T18_8_gfblup_variances_all_4001_5000.rds") +T18_8_gfblup_variances_all_5001_6000=readRDS(file="T18_8_gfblup_variances_all_5001_6000.rds") +T18_8_gfblup_variances_all_6001_7297=readRDS(file="T18_8_gfblup_variances_all_6001_7297.rds") + +cycles=length(T18_8_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T18_8_gfblup_variances_all=rep(list(list()),cycles) +T18_8_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_1_1000[[r]]) + T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_1001_2000[[r]]) + T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_2001_3000[[r]]) + T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_3001_4000[[r]]) + T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_4001_5000[[r]]) + T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_5001_6000[[r]]) + T18_8_gfblup_prediction_all[[r]]<-c(T18_8_gfblup_prediction_all[[r]],T18_8_gfblup_prediction_all_6001_7297[[r]]) + + T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_1_1000[[r]]) + T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_1001_2000[[r]]) + T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_2001_3000[[r]]) + T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_3001_4000[[r]]) + T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_4001_5000[[r]]) + T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_5001_6000[[r]]) + T18_8_gfblup_variances_all[[r]]<-c(T18_8_gfblup_variances_all[[r]],T18_8_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T18_8_gfblup_prediction_all,"T18_8_gfblup_prediction_all.rds") +saveRDS(T18_8_gfblup_variances_all,"T18_8_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_1_gblup_prediction_all_1_1000=readRDS(file="T19_1_gblup_prediction_all_1_1000.rds") +T19_1_gblup_prediction_all_1001_2000=readRDS(file="T19_1_gblup_prediction_all_1001_2000.rds") +T19_1_gblup_prediction_all_2001_3000=readRDS(file="T19_1_gblup_prediction_all_2001_3000.rds") +T19_1_gblup_prediction_all_3001_4000=readRDS(file="T19_1_gblup_prediction_all_3001_4000.rds") +T19_1_gblup_prediction_all_4001_5000=readRDS(file="T19_1_gblup_prediction_all_4001_5000.rds") +T19_1_gblup_prediction_all_5001_6000=readRDS(file="T19_1_gblup_prediction_all_5001_6000.rds") +T19_1_gblup_prediction_all_6001_7297=readRDS(file="T19_1_gblup_prediction_all_6001_7297.rds") +T19_1_gblup_prediction_all=c(T19_1_gblup_prediction_all_1_1000,T19_1_gblup_prediction_all_1001_2000,T19_1_gblup_prediction_all_2001_3000,T19_1_gblup_prediction_all_3001_4000,T19_1_gblup_prediction_all_4001_5000,T19_1_gblup_prediction_all_5001_6000,T19_1_gblup_prediction_all_6001_7297) + +T19_1_gblup_variances_all_1_1000=readRDS(file="T19_1_gblup_variances_all_1_1000.rds") +T19_1_gblup_variances_all_1001_2000=readRDS(file="T19_1_gblup_variances_all_1001_2000.rds") +T19_1_gblup_variances_all_2001_3000=readRDS(file="T19_1_gblup_variances_all_2001_3000.rds") +T19_1_gblup_variances_all_3001_4000=readRDS(file="T19_1_gblup_variances_all_3001_4000.rds") +T19_1_gblup_variances_all_4001_5000=readRDS(file="T19_1_gblup_variances_all_4001_5000.rds") +T19_1_gblup_variances_all_5001_6000=readRDS(file="T19_1_gblup_variances_all_5001_6000.rds") +T19_1_gblup_variances_all_6001_7297=readRDS(file="T19_1_gblup_variances_all_6001_7297.rds") +T19_1_gblup_variances_all=c(T19_1_gblup_variances_all_1_1000,T19_1_gblup_variances_all_1001_2000,T19_1_gblup_variances_all_2001_3000,T19_1_gblup_variances_all_3001_4000,T19_1_gblup_variances_all_4001_5000,T19_1_gblup_variances_all_5001_6000,T19_1_gblup_variances_all_6001_7297) + +saveRDS(T19_1_gblup_prediction_all,"T19_1_gblup_prediction_all.rds") +saveRDS(T19_1_gblup_variances_all,"T19_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_1_gfblup_prediction_all_1_1000=readRDS(file="T19_1_gfblup_prediction_all_1_1000.rds") +T19_1_gfblup_prediction_all_1001_2000=readRDS(file="T19_1_gfblup_prediction_all_1001_2000.rds") +T19_1_gfblup_prediction_all_2001_3000=readRDS(file="T19_1_gfblup_prediction_all_2001_3000.rds") +T19_1_gfblup_prediction_all_3001_4000=readRDS(file="T19_1_gfblup_prediction_all_3001_4000.rds") +T19_1_gfblup_prediction_all_4001_5000=readRDS(file="T19_1_gfblup_prediction_all_4001_5000.rds") +T19_1_gfblup_prediction_all_5001_6000=readRDS(file="T19_1_gfblup_prediction_all_5001_6000.rds") +T19_1_gfblup_prediction_all_6001_7297=readRDS(file="T19_1_gfblup_prediction_all_6001_7297.rds") + +T19_1_gfblup_variances_all_1_1000=readRDS(file="T19_1_gfblup_variances_all_1_1000.rds") +T19_1_gfblup_variances_all_1001_2000=readRDS(file="T19_1_gfblup_variances_all_1001_2000.rds") +T19_1_gfblup_variances_all_2001_3000=readRDS(file="T19_1_gfblup_variances_all_2001_3000.rds") +T19_1_gfblup_variances_all_3001_4000=readRDS(file="T19_1_gfblup_variances_all_3001_4000.rds") +T19_1_gfblup_variances_all_4001_5000=readRDS(file="T19_1_gfblup_variances_all_4001_5000.rds") +T19_1_gfblup_variances_all_5001_6000=readRDS(file="T19_1_gfblup_variances_all_5001_6000.rds") +T19_1_gfblup_variances_all_6001_7297=readRDS(file="T19_1_gfblup_variances_all_6001_7297.rds") + +cycles=length(T19_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T19_1_gfblup_variances_all=rep(list(list()),cycles) +T19_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_1_1000[[r]]) + T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_1001_2000[[r]]) + T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_2001_3000[[r]]) + T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_3001_4000[[r]]) + T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_4001_5000[[r]]) + T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_5001_6000[[r]]) + T19_1_gfblup_prediction_all[[r]]<-c(T19_1_gfblup_prediction_all[[r]],T19_1_gfblup_prediction_all_6001_7297[[r]]) + + T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_1_1000[[r]]) + T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_1001_2000[[r]]) + T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_2001_3000[[r]]) + T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_3001_4000[[r]]) + T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_4001_5000[[r]]) + T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_5001_6000[[r]]) + T19_1_gfblup_variances_all[[r]]<-c(T19_1_gfblup_variances_all[[r]],T19_1_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T19_1_gfblup_prediction_all,"T19_1_gfblup_prediction_all.rds") +saveRDS(T19_1_gfblup_variances_all,"T19_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_2_gblup_prediction_all_1_1000=readRDS(file="T19_2_gblup_prediction_all_1_1000.rds") +T19_2_gblup_prediction_all_1001_2000=readRDS(file="T19_2_gblup_prediction_all_1001_2000.rds") +T19_2_gblup_prediction_all_2001_3000=readRDS(file="T19_2_gblup_prediction_all_2001_3000.rds") +T19_2_gblup_prediction_all_3001_4000=readRDS(file="T19_2_gblup_prediction_all_3001_4000.rds") +T19_2_gblup_prediction_all_4001_5000=readRDS(file="T19_2_gblup_prediction_all_4001_5000.rds") +T19_2_gblup_prediction_all_5001_6000=readRDS(file="T19_2_gblup_prediction_all_5001_6000.rds") +T19_2_gblup_prediction_all_6001_7297=readRDS(file="T19_2_gblup_prediction_all_6001_7297.rds") +T19_2_gblup_prediction_all=c(T19_2_gblup_prediction_all_1_1000,T19_2_gblup_prediction_all_1001_2000,T19_2_gblup_prediction_all_2001_3000,T19_2_gblup_prediction_all_3001_4000,T19_2_gblup_prediction_all_4001_5000,T19_2_gblup_prediction_all_5001_6000,T19_2_gblup_prediction_all_6001_7297) + +T19_2_gblup_variances_all_1_1000=readRDS(file="T19_2_gblup_variances_all_1_1000.rds") +T19_2_gblup_variances_all_1001_2000=readRDS(file="T19_2_gblup_variances_all_1001_2000.rds") +T19_2_gblup_variances_all_2001_3000=readRDS(file="T19_2_gblup_variances_all_2001_3000.rds") +T19_2_gblup_variances_all_3001_4000=readRDS(file="T19_2_gblup_variances_all_3001_4000.rds") +T19_2_gblup_variances_all_4001_5000=readRDS(file="T19_2_gblup_variances_all_4001_5000.rds") +T19_2_gblup_variances_all_5001_6000=readRDS(file="T19_2_gblup_variances_all_5001_6000.rds") +T19_2_gblup_variances_all_6001_7297=readRDS(file="T19_2_gblup_variances_all_6001_7297.rds") +T19_2_gblup_variances_all=c(T19_2_gblup_variances_all_1_1000,T19_2_gblup_variances_all_1001_2000,T19_2_gblup_variances_all_2001_3000,T19_2_gblup_variances_all_3001_4000,T19_2_gblup_variances_all_4001_5000,T19_2_gblup_variances_all_5001_6000,T19_2_gblup_variances_all_6001_7297) + +saveRDS(T19_2_gblup_prediction_all,"T19_2_gblup_prediction_all.rds") +saveRDS(T19_2_gblup_variances_all,"T19_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_2_gfblup_prediction_all_1_1000=readRDS(file="T19_2_gfblup_prediction_all_1_1000.rds") +T19_2_gfblup_prediction_all_1001_2000=readRDS(file="T19_2_gfblup_prediction_all_1001_2000.rds") +T19_2_gfblup_prediction_all_2001_3000=readRDS(file="T19_2_gfblup_prediction_all_2001_3000.rds") +T19_2_gfblup_prediction_all_3001_4000=readRDS(file="T19_2_gfblup_prediction_all_3001_4000.rds") +T19_2_gfblup_prediction_all_4001_5000=readRDS(file="T19_2_gfblup_prediction_all_4001_5000.rds") +T19_2_gfblup_prediction_all_5001_6000=readRDS(file="T19_2_gfblup_prediction_all_5001_6000.rds") +T19_2_gfblup_prediction_all_6001_7297=readRDS(file="T19_2_gfblup_prediction_all_6001_7297.rds") + +T19_2_gfblup_variances_all_1_1000=readRDS(file="T19_2_gfblup_variances_all_1_1000.rds") +T19_2_gfblup_variances_all_1001_2000=readRDS(file="T19_2_gfblup_variances_all_1001_2000.rds") +T19_2_gfblup_variances_all_2001_3000=readRDS(file="T19_2_gfblup_variances_all_2001_3000.rds") +T19_2_gfblup_variances_all_3001_4000=readRDS(file="T19_2_gfblup_variances_all_3001_4000.rds") +T19_2_gfblup_variances_all_4001_5000=readRDS(file="T19_2_gfblup_variances_all_4001_5000.rds") +T19_2_gfblup_variances_all_5001_6000=readRDS(file="T19_2_gfblup_variances_all_5001_6000.rds") +T19_2_gfblup_variances_all_6001_7297=readRDS(file="T19_2_gfblup_variances_all_6001_7297.rds") + +cycles=length(T19_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T19_2_gfblup_variances_all=rep(list(list()),cycles) +T19_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_1_1000[[r]]) + T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_1001_2000[[r]]) + T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_2001_3000[[r]]) + T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_3001_4000[[r]]) + T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_4001_5000[[r]]) + T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_5001_6000[[r]]) + T19_2_gfblup_prediction_all[[r]]<-c(T19_2_gfblup_prediction_all[[r]],T19_2_gfblup_prediction_all_6001_7297[[r]]) + + T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_1_1000[[r]]) + T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_1001_2000[[r]]) + T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_2001_3000[[r]]) + T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_3001_4000[[r]]) + T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_4001_5000[[r]]) + T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_5001_6000[[r]]) + T19_2_gfblup_variances_all[[r]]<-c(T19_2_gfblup_variances_all[[r]],T19_2_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T19_2_gfblup_prediction_all,"T19_2_gfblup_prediction_all.rds") +saveRDS(T19_2_gfblup_variances_all,"T19_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_3_gblup_prediction_all_1_1000=readRDS(file="T19_3_gblup_prediction_all_1_1000.rds") +T19_3_gblup_prediction_all_1001_2000=readRDS(file="T19_3_gblup_prediction_all_1001_2000.rds") +T19_3_gblup_prediction_all_2001_3000=readRDS(file="T19_3_gblup_prediction_all_2001_3000.rds") +T19_3_gblup_prediction_all_3001_4000=readRDS(file="T19_3_gblup_prediction_all_3001_4000.rds") +T19_3_gblup_prediction_all_4001_5000=readRDS(file="T19_3_gblup_prediction_all_4001_5000.rds") +T19_3_gblup_prediction_all_5001_6000=readRDS(file="T19_3_gblup_prediction_all_5001_6000.rds") +T19_3_gblup_prediction_all_6001_7297=readRDS(file="T19_3_gblup_prediction_all_6001_7297.rds") +T19_3_gblup_prediction_all=c(T19_3_gblup_prediction_all_1_1000,T19_3_gblup_prediction_all_1001_2000,T19_3_gblup_prediction_all_2001_3000,T19_3_gblup_prediction_all_3001_4000,T19_3_gblup_prediction_all_4001_5000,T19_3_gblup_prediction_all_5001_6000,T19_3_gblup_prediction_all_6001_7297) + +T19_3_gblup_variances_all_1_1000=readRDS(file="T19_3_gblup_variances_all_1_1000.rds") +T19_3_gblup_variances_all_1001_2000=readRDS(file="T19_3_gblup_variances_all_1001_2000.rds") +T19_3_gblup_variances_all_2001_3000=readRDS(file="T19_3_gblup_variances_all_2001_3000.rds") +T19_3_gblup_variances_all_3001_4000=readRDS(file="T19_3_gblup_variances_all_3001_4000.rds") +T19_3_gblup_variances_all_4001_5000=readRDS(file="T19_3_gblup_variances_all_4001_5000.rds") +T19_3_gblup_variances_all_5001_6000=readRDS(file="T19_3_gblup_variances_all_5001_6000.rds") +T19_3_gblup_variances_all_6001_7297=readRDS(file="T19_3_gblup_variances_all_6001_7297.rds") +T19_3_gblup_variances_all=c(T19_3_gblup_variances_all_1_1000,T19_3_gblup_variances_all_1001_2000,T19_3_gblup_variances_all_2001_3000,T19_3_gblup_variances_all_3001_4000,T19_3_gblup_variances_all_4001_5000,T19_3_gblup_variances_all_5001_6000,T19_3_gblup_variances_all_6001_7297) + +saveRDS(T19_3_gblup_prediction_all,"T19_3_gblup_prediction_all.rds") +saveRDS(T19_3_gblup_variances_all,"T19_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_3_gfblup_prediction_all_1_1000=readRDS(file="T19_3_gfblup_prediction_all_1_1000.rds") +T19_3_gfblup_prediction_all_1001_2000=readRDS(file="T19_3_gfblup_prediction_all_1001_2000.rds") +T19_3_gfblup_prediction_all_2001_3000=readRDS(file="T19_3_gfblup_prediction_all_2001_3000.rds") +T19_3_gfblup_prediction_all_3001_4000=readRDS(file="T19_3_gfblup_prediction_all_3001_4000.rds") +T19_3_gfblup_prediction_all_4001_5000=readRDS(file="T19_3_gfblup_prediction_all_4001_5000.rds") +T19_3_gfblup_prediction_all_5001_6000=readRDS(file="T19_3_gfblup_prediction_all_5001_6000.rds") +T19_3_gfblup_prediction_all_6001_7297=readRDS(file="T19_3_gfblup_prediction_all_6001_7297.rds") + +T19_3_gfblup_variances_all_1_1000=readRDS(file="T19_3_gfblup_variances_all_1_1000.rds") +T19_3_gfblup_variances_all_1001_2000=readRDS(file="T19_3_gfblup_variances_all_1001_2000.rds") +T19_3_gfblup_variances_all_2001_3000=readRDS(file="T19_3_gfblup_variances_all_2001_3000.rds") +T19_3_gfblup_variances_all_3001_4000=readRDS(file="T19_3_gfblup_variances_all_3001_4000.rds") +T19_3_gfblup_variances_all_4001_5000=readRDS(file="T19_3_gfblup_variances_all_4001_5000.rds") +T19_3_gfblup_variances_all_5001_6000=readRDS(file="T19_3_gfblup_variances_all_5001_6000.rds") +T19_3_gfblup_variances_all_6001_7297=readRDS(file="T19_3_gfblup_variances_all_6001_7297.rds") + +cycles=length(T19_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T19_3_gfblup_variances_all=rep(list(list()),cycles) +T19_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_1_1000[[r]]) + T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_1001_2000[[r]]) + T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_2001_3000[[r]]) + T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_3001_4000[[r]]) + T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_4001_5000[[r]]) + T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_5001_6000[[r]]) + T19_3_gfblup_prediction_all[[r]]<-c(T19_3_gfblup_prediction_all[[r]],T19_3_gfblup_prediction_all_6001_7297[[r]]) + + T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_1_1000[[r]]) + T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_1001_2000[[r]]) + T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_2001_3000[[r]]) + T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_3001_4000[[r]]) + T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_4001_5000[[r]]) + T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_5001_6000[[r]]) + T19_3_gfblup_variances_all[[r]]<-c(T19_3_gfblup_variances_all[[r]],T19_3_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T19_3_gfblup_prediction_all,"T19_3_gfblup_prediction_all.rds") +saveRDS(T19_3_gfblup_variances_all,"T19_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_4_gblup_prediction_all_1_1000=readRDS(file="T19_4_gblup_prediction_all_1_1000.rds") +T19_4_gblup_prediction_all_1001_2000=readRDS(file="T19_4_gblup_prediction_all_1001_2000.rds") +T19_4_gblup_prediction_all_2001_3000=readRDS(file="T19_4_gblup_prediction_all_2001_3000.rds") +T19_4_gblup_prediction_all_3001_4000=readRDS(file="T19_4_gblup_prediction_all_3001_4000.rds") +T19_4_gblup_prediction_all_4001_5000=readRDS(file="T19_4_gblup_prediction_all_4001_5000.rds") +T19_4_gblup_prediction_all_5001_6000=readRDS(file="T19_4_gblup_prediction_all_5001_6000.rds") +T19_4_gblup_prediction_all_6001_7297=readRDS(file="T19_4_gblup_prediction_all_6001_7297.rds") +T19_4_gblup_prediction_all=c(T19_4_gblup_prediction_all_1_1000,T19_4_gblup_prediction_all_1001_2000,T19_4_gblup_prediction_all_2001_3000,T19_4_gblup_prediction_all_3001_4000,T19_4_gblup_prediction_all_4001_5000,T19_4_gblup_prediction_all_5001_6000,T19_4_gblup_prediction_all_6001_7297) + +T19_4_gblup_variances_all_1_1000=readRDS(file="T19_4_gblup_variances_all_1_1000.rds") +T19_4_gblup_variances_all_1001_2000=readRDS(file="T19_4_gblup_variances_all_1001_2000.rds") +T19_4_gblup_variances_all_2001_3000=readRDS(file="T19_4_gblup_variances_all_2001_3000.rds") +T19_4_gblup_variances_all_3001_4000=readRDS(file="T19_4_gblup_variances_all_3001_4000.rds") +T19_4_gblup_variances_all_4001_5000=readRDS(file="T19_4_gblup_variances_all_4001_5000.rds") +T19_4_gblup_variances_all_5001_6000=readRDS(file="T19_4_gblup_variances_all_5001_6000.rds") +T19_4_gblup_variances_all_6001_7297=readRDS(file="T19_4_gblup_variances_all_6001_7297.rds") +T19_4_gblup_variances_all=c(T19_4_gblup_variances_all_1_1000,T19_4_gblup_variances_all_1001_2000,T19_4_gblup_variances_all_2001_3000,T19_4_gblup_variances_all_3001_4000,T19_4_gblup_variances_all_4001_5000,T19_4_gblup_variances_all_5001_6000,T19_4_gblup_variances_all_6001_7297) + +saveRDS(T19_4_gblup_prediction_all,"T19_4_gblup_prediction_all.rds") +saveRDS(T19_4_gblup_variances_all,"T19_4_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_4_gfblup_prediction_all_1_1000=readRDS(file="T19_4_gfblup_prediction_all_1_1000.rds") +T19_4_gfblup_prediction_all_1001_2000=readRDS(file="T19_4_gfblup_prediction_all_1001_2000.rds") +T19_4_gfblup_prediction_all_2001_3000=readRDS(file="T19_4_gfblup_prediction_all_2001_3000.rds") +T19_4_gfblup_prediction_all_3001_4000=readRDS(file="T19_4_gfblup_prediction_all_3001_4000.rds") +T19_4_gfblup_prediction_all_4001_5000=readRDS(file="T19_4_gfblup_prediction_all_4001_5000.rds") +T19_4_gfblup_prediction_all_5001_6000=readRDS(file="T19_4_gfblup_prediction_all_5001_6000.rds") +T19_4_gfblup_prediction_all_6001_7297=readRDS(file="T19_4_gfblup_prediction_all_6001_7297.rds") + +T19_4_gfblup_variances_all_1_1000=readRDS(file="T19_4_gfblup_variances_all_1_1000.rds") +T19_4_gfblup_variances_all_1001_2000=readRDS(file="T19_4_gfblup_variances_all_1001_2000.rds") +T19_4_gfblup_variances_all_2001_3000=readRDS(file="T19_4_gfblup_variances_all_2001_3000.rds") +T19_4_gfblup_variances_all_3001_4000=readRDS(file="T19_4_gfblup_variances_all_3001_4000.rds") +T19_4_gfblup_variances_all_4001_5000=readRDS(file="T19_4_gfblup_variances_all_4001_5000.rds") +T19_4_gfblup_variances_all_5001_6000=readRDS(file="T19_4_gfblup_variances_all_5001_6000.rds") +T19_4_gfblup_variances_all_6001_7297=readRDS(file="T19_4_gfblup_variances_all_6001_7297.rds") + +cycles=length(T19_4_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T19_4_gfblup_variances_all=rep(list(list()),cycles) +T19_4_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_1_1000[[r]]) + T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_1001_2000[[r]]) + T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_2001_3000[[r]]) + T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_3001_4000[[r]]) + T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_4001_5000[[r]]) + T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_5001_6000[[r]]) + T19_4_gfblup_prediction_all[[r]]<-c(T19_4_gfblup_prediction_all[[r]],T19_4_gfblup_prediction_all_6001_7297[[r]]) + + T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_1_1000[[r]]) + T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_1001_2000[[r]]) + T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_2001_3000[[r]]) + T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_3001_4000[[r]]) + T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_4001_5000[[r]]) + T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_5001_6000[[r]]) + T19_4_gfblup_variances_all[[r]]<-c(T19_4_gfblup_variances_all[[r]],T19_4_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T19_4_gfblup_prediction_all,"T19_4_gfblup_prediction_all.rds") +saveRDS(T19_4_gfblup_variances_all,"T19_4_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_5_gblup_prediction_all_1_1000=readRDS(file="T19_5_gblup_prediction_all_1_1000.rds") +T19_5_gblup_prediction_all_1001_2000=readRDS(file="T19_5_gblup_prediction_all_1001_2000.rds") +T19_5_gblup_prediction_all_2001_3000=readRDS(file="T19_5_gblup_prediction_all_2001_3000.rds") +T19_5_gblup_prediction_all_3001_4000=readRDS(file="T19_5_gblup_prediction_all_3001_4000.rds") +T19_5_gblup_prediction_all_4001_5000=readRDS(file="T19_5_gblup_prediction_all_4001_5000.rds") +T19_5_gblup_prediction_all_5001_6000=readRDS(file="T19_5_gblup_prediction_all_5001_6000.rds") +T19_5_gblup_prediction_all_6001_7297=readRDS(file="T19_5_gblup_prediction_all_6001_7297.rds") +T19_5_gblup_prediction_all=c(T19_5_gblup_prediction_all_1_1000,T19_5_gblup_prediction_all_1001_2000,T19_5_gblup_prediction_all_2001_3000,T19_5_gblup_prediction_all_3001_4000,T19_5_gblup_prediction_all_4001_5000,T19_5_gblup_prediction_all_5001_6000,T19_5_gblup_prediction_all_6001_7297) + +T19_5_gblup_variances_all_1_1000=readRDS(file="T19_5_gblup_variances_all_1_1000.rds") +T19_5_gblup_variances_all_1001_2000=readRDS(file="T19_5_gblup_variances_all_1001_2000.rds") +T19_5_gblup_variances_all_2001_3000=readRDS(file="T19_5_gblup_variances_all_2001_3000.rds") +T19_5_gblup_variances_all_3001_4000=readRDS(file="T19_5_gblup_variances_all_3001_4000.rds") +T19_5_gblup_variances_all_4001_5000=readRDS(file="T19_5_gblup_variances_all_4001_5000.rds") +T19_5_gblup_variances_all_5001_6000=readRDS(file="T19_5_gblup_variances_all_5001_6000.rds") +T19_5_gblup_variances_all_6001_7297=readRDS(file="T19_5_gblup_variances_all_6001_7297.rds") +T19_5_gblup_variances_all=c(T19_5_gblup_variances_all_1_1000,T19_5_gblup_variances_all_1001_2000,T19_5_gblup_variances_all_2001_3000,T19_5_gblup_variances_all_3001_4000,T19_5_gblup_variances_all_4001_5000,T19_5_gblup_variances_all_5001_6000,T19_5_gblup_variances_all_6001_7297) + +saveRDS(T19_5_gblup_prediction_all,"T19_5_gblup_prediction_all.rds") +saveRDS(T19_5_gblup_variances_all,"T19_5_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_5_gfblup_prediction_all_1_1000=readRDS(file="T19_5_gfblup_prediction_all_1_1000.rds") +T19_5_gfblup_prediction_all_1001_2000=readRDS(file="T19_5_gfblup_prediction_all_1001_2000.rds") +T19_5_gfblup_prediction_all_2001_3000=readRDS(file="T19_5_gfblup_prediction_all_2001_3000.rds") +T19_5_gfblup_prediction_all_3001_4000=readRDS(file="T19_5_gfblup_prediction_all_3001_4000.rds") +T19_5_gfblup_prediction_all_4001_5000=readRDS(file="T19_5_gfblup_prediction_all_4001_5000.rds") +T19_5_gfblup_prediction_all_5001_6000=readRDS(file="T19_5_gfblup_prediction_all_5001_6000.rds") +T19_5_gfblup_prediction_all_6001_7297=readRDS(file="T19_5_gfblup_prediction_all_6001_7297.rds") + +T19_5_gfblup_variances_all_1_1000=readRDS(file="T19_5_gfblup_variances_all_1_1000.rds") +T19_5_gfblup_variances_all_1001_2000=readRDS(file="T19_5_gfblup_variances_all_1001_2000.rds") +T19_5_gfblup_variances_all_2001_3000=readRDS(file="T19_5_gfblup_variances_all_2001_3000.rds") +T19_5_gfblup_variances_all_3001_4000=readRDS(file="T19_5_gfblup_variances_all_3001_4000.rds") +T19_5_gfblup_variances_all_4001_5000=readRDS(file="T19_5_gfblup_variances_all_4001_5000.rds") +T19_5_gfblup_variances_all_5001_6000=readRDS(file="T19_5_gfblup_variances_all_5001_6000.rds") +T19_5_gfblup_variances_all_6001_7297=readRDS(file="T19_5_gfblup_variances_all_6001_7297.rds") + +cycles=length(T19_5_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T19_5_gfblup_variances_all=rep(list(list()),cycles) +T19_5_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_1_1000[[r]]) + T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_1001_2000[[r]]) + T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_2001_3000[[r]]) + T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_3001_4000[[r]]) + T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_4001_5000[[r]]) + T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_5001_6000[[r]]) + T19_5_gfblup_prediction_all[[r]]<-c(T19_5_gfblup_prediction_all[[r]],T19_5_gfblup_prediction_all_6001_7297[[r]]) + + T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_1_1000[[r]]) + T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_1001_2000[[r]]) + T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_2001_3000[[r]]) + T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_3001_4000[[r]]) + T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_4001_5000[[r]]) + T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_5001_6000[[r]]) + T19_5_gfblup_variances_all[[r]]<-c(T19_5_gfblup_variances_all[[r]],T19_5_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T19_5_gfblup_prediction_all,"T19_5_gfblup_prediction_all.rds") +saveRDS(T19_5_gfblup_variances_all,"T19_5_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_6_gblup_prediction_all_1_1000=readRDS(file="T19_6_gblup_prediction_all_1_1000.rds") +T19_6_gblup_prediction_all_1001_2000=readRDS(file="T19_6_gblup_prediction_all_1001_2000.rds") +T19_6_gblup_prediction_all_2001_3000=readRDS(file="T19_6_gblup_prediction_all_2001_3000.rds") +T19_6_gblup_prediction_all_3001_4000=readRDS(file="T19_6_gblup_prediction_all_3001_4000.rds") +T19_6_gblup_prediction_all_4001_5000=readRDS(file="T19_6_gblup_prediction_all_4001_5000.rds") +T19_6_gblup_prediction_all_5001_6000=readRDS(file="T19_6_gblup_prediction_all_5001_6000.rds") +T19_6_gblup_prediction_all_6001_7297=readRDS(file="T19_6_gblup_prediction_all_6001_7297.rds") +T19_6_gblup_prediction_all=c(T19_6_gblup_prediction_all_1_1000,T19_6_gblup_prediction_all_1001_2000,T19_6_gblup_prediction_all_2001_3000,T19_6_gblup_prediction_all_3001_4000,T19_6_gblup_prediction_all_4001_5000,T19_6_gblup_prediction_all_5001_6000,T19_6_gblup_prediction_all_6001_7297) + +T19_6_gblup_variances_all_1_1000=readRDS(file="T19_6_gblup_variances_all_1_1000.rds") +T19_6_gblup_variances_all_1001_2000=readRDS(file="T19_6_gblup_variances_all_1001_2000.rds") +T19_6_gblup_variances_all_2001_3000=readRDS(file="T19_6_gblup_variances_all_2001_3000.rds") +T19_6_gblup_variances_all_3001_4000=readRDS(file="T19_6_gblup_variances_all_3001_4000.rds") +T19_6_gblup_variances_all_4001_5000=readRDS(file="T19_6_gblup_variances_all_4001_5000.rds") +T19_6_gblup_variances_all_5001_6000=readRDS(file="T19_6_gblup_variances_all_5001_6000.rds") +T19_6_gblup_variances_all_6001_7297=readRDS(file="T19_6_gblup_variances_all_6001_7297.rds") +T19_6_gblup_variances_all=c(T19_6_gblup_variances_all_1_1000,T19_6_gblup_variances_all_1001_2000,T19_6_gblup_variances_all_2001_3000,T19_6_gblup_variances_all_3001_4000,T19_6_gblup_variances_all_4001_5000,T19_6_gblup_variances_all_5001_6000,T19_6_gblup_variances_all_6001_7297) + +saveRDS(T19_6_gblup_prediction_all,"T19_6_gblup_prediction_all.rds") +saveRDS(T19_6_gblup_variances_all,"T19_6_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_6_gfblup_prediction_all_1_1000=readRDS(file="T19_6_gfblup_prediction_all_1_1000.rds") +T19_6_gfblup_prediction_all_1001_2000=readRDS(file="T19_6_gfblup_prediction_all_1001_2000.rds") +T19_6_gfblup_prediction_all_2001_3000=readRDS(file="T19_6_gfblup_prediction_all_2001_3000.rds") +T19_6_gfblup_prediction_all_3001_4000=readRDS(file="T19_6_gfblup_prediction_all_3001_4000.rds") +T19_6_gfblup_prediction_all_4001_5000=readRDS(file="T19_6_gfblup_prediction_all_4001_5000.rds") +T19_6_gfblup_prediction_all_5001_6000=readRDS(file="T19_6_gfblup_prediction_all_5001_6000.rds") +T19_6_gfblup_prediction_all_6001_7297=readRDS(file="T19_6_gfblup_prediction_all_6001_7297.rds") + +T19_6_gfblup_variances_all_1_1000=readRDS(file="T19_6_gfblup_variances_all_1_1000.rds") +T19_6_gfblup_variances_all_1001_2000=readRDS(file="T19_6_gfblup_variances_all_1001_2000.rds") +T19_6_gfblup_variances_all_2001_3000=readRDS(file="T19_6_gfblup_variances_all_2001_3000.rds") +T19_6_gfblup_variances_all_3001_4000=readRDS(file="T19_6_gfblup_variances_all_3001_4000.rds") +T19_6_gfblup_variances_all_4001_5000=readRDS(file="T19_6_gfblup_variances_all_4001_5000.rds") +T19_6_gfblup_variances_all_5001_6000=readRDS(file="T19_6_gfblup_variances_all_5001_6000.rds") +T19_6_gfblup_variances_all_6001_7297=readRDS(file="T19_6_gfblup_variances_all_6001_7297.rds") + +cycles=length(T19_6_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T19_6_gfblup_variances_all=rep(list(list()),cycles) +T19_6_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_1_1000[[r]]) + T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_1001_2000[[r]]) + T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_2001_3000[[r]]) + T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_3001_4000[[r]]) + T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_4001_5000[[r]]) + T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_5001_6000[[r]]) + T19_6_gfblup_prediction_all[[r]]<-c(T19_6_gfblup_prediction_all[[r]],T19_6_gfblup_prediction_all_6001_7297[[r]]) + + T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_1_1000[[r]]) + T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_1001_2000[[r]]) + T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_2001_3000[[r]]) + T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_3001_4000[[r]]) + T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_4001_5000[[r]]) + T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_5001_6000[[r]]) + T19_6_gfblup_variances_all[[r]]<-c(T19_6_gfblup_variances_all[[r]],T19_6_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T19_6_gfblup_prediction_all,"T19_6_gfblup_prediction_all.rds") +saveRDS(T19_6_gfblup_variances_all,"T19_6_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_7_gblup_prediction_all_1_1000=readRDS(file="T19_7_gblup_prediction_all_1_1000.rds") +T19_7_gblup_prediction_all_1001_2000=readRDS(file="T19_7_gblup_prediction_all_1001_2000.rds") +T19_7_gblup_prediction_all_2001_3000=readRDS(file="T19_7_gblup_prediction_all_2001_3000.rds") +T19_7_gblup_prediction_all_3001_4000=readRDS(file="T19_7_gblup_prediction_all_3001_4000.rds") +T19_7_gblup_prediction_all_4001_5000=readRDS(file="T19_7_gblup_prediction_all_4001_5000.rds") +T19_7_gblup_prediction_all_5001_6000=readRDS(file="T19_7_gblup_prediction_all_5001_6000.rds") +T19_7_gblup_prediction_all_6001_7297=readRDS(file="T19_7_gblup_prediction_all_6001_7297.rds") +T19_7_gblup_prediction_all=c(T19_7_gblup_prediction_all_1_1000,T19_7_gblup_prediction_all_1001_2000,T19_7_gblup_prediction_all_2001_3000,T19_7_gblup_prediction_all_3001_4000,T19_7_gblup_prediction_all_4001_5000,T19_7_gblup_prediction_all_5001_6000,T19_7_gblup_prediction_all_6001_7297) + +T19_7_gblup_variances_all_1_1000=readRDS(file="T19_7_gblup_variances_all_1_1000.rds") +T19_7_gblup_variances_all_1001_2000=readRDS(file="T19_7_gblup_variances_all_1001_2000.rds") +T19_7_gblup_variances_all_2001_3000=readRDS(file="T19_7_gblup_variances_all_2001_3000.rds") +T19_7_gblup_variances_all_3001_4000=readRDS(file="T19_7_gblup_variances_all_3001_4000.rds") +T19_7_gblup_variances_all_4001_5000=readRDS(file="T19_7_gblup_variances_all_4001_5000.rds") +T19_7_gblup_variances_all_5001_6000=readRDS(file="T19_7_gblup_variances_all_5001_6000.rds") +T19_7_gblup_variances_all_6001_7297=readRDS(file="T19_7_gblup_variances_all_6001_7297.rds") +T19_7_gblup_variances_all=c(T19_7_gblup_variances_all_1_1000,T19_7_gblup_variances_all_1001_2000,T19_7_gblup_variances_all_2001_3000,T19_7_gblup_variances_all_3001_4000,T19_7_gblup_variances_all_4001_5000,T19_7_gblup_variances_all_5001_6000,T19_7_gblup_variances_all_6001_7297) + +saveRDS(T19_7_gblup_prediction_all,"T19_7_gblup_prediction_all.rds") +saveRDS(T19_7_gblup_variances_all,"T19_7_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_7_gfblup_prediction_all_1_1000=readRDS(file="T19_7_gfblup_prediction_all_1_1000.rds") +T19_7_gfblup_prediction_all_1001_2000=readRDS(file="T19_7_gfblup_prediction_all_1001_2000.rds") +T19_7_gfblup_prediction_all_2001_3000=readRDS(file="T19_7_gfblup_prediction_all_2001_3000.rds") +T19_7_gfblup_prediction_all_3001_4000=readRDS(file="T19_7_gfblup_prediction_all_3001_4000.rds") +T19_7_gfblup_prediction_all_4001_5000=readRDS(file="T19_7_gfblup_prediction_all_4001_5000.rds") +T19_7_gfblup_prediction_all_5001_6000=readRDS(file="T19_7_gfblup_prediction_all_5001_6000.rds") +T19_7_gfblup_prediction_all_6001_7297=readRDS(file="T19_7_gfblup_prediction_all_6001_7297.rds") + +T19_7_gfblup_variances_all_1_1000=readRDS(file="T19_7_gfblup_variances_all_1_1000.rds") +T19_7_gfblup_variances_all_1001_2000=readRDS(file="T19_7_gfblup_variances_all_1001_2000.rds") +T19_7_gfblup_variances_all_2001_3000=readRDS(file="T19_7_gfblup_variances_all_2001_3000.rds") +T19_7_gfblup_variances_all_3001_4000=readRDS(file="T19_7_gfblup_variances_all_3001_4000.rds") +T19_7_gfblup_variances_all_4001_5000=readRDS(file="T19_7_gfblup_variances_all_4001_5000.rds") +T19_7_gfblup_variances_all_5001_6000=readRDS(file="T19_7_gfblup_variances_all_5001_6000.rds") +T19_7_gfblup_variances_all_6001_7297=readRDS(file="T19_7_gfblup_variances_all_6001_7297.rds") + +cycles=length(T19_7_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T19_7_gfblup_variances_all=rep(list(list()),cycles) +T19_7_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_1_1000[[r]]) + T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_1001_2000[[r]]) + T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_2001_3000[[r]]) + T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_3001_4000[[r]]) + T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_4001_5000[[r]]) + T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_5001_6000[[r]]) + T19_7_gfblup_prediction_all[[r]]<-c(T19_7_gfblup_prediction_all[[r]],T19_7_gfblup_prediction_all_6001_7297[[r]]) + + T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_1_1000[[r]]) + T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_1001_2000[[r]]) + T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_2001_3000[[r]]) + T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_3001_4000[[r]]) + T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_4001_5000[[r]]) + T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_5001_6000[[r]]) + T19_7_gfblup_variances_all[[r]]<-c(T19_7_gfblup_variances_all[[r]],T19_7_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T19_7_gfblup_prediction_all,"T19_7_gfblup_prediction_all.rds") +saveRDS(T19_7_gfblup_variances_all,"T19_7_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_8_gblup_prediction_all_1_1000=readRDS(file="T19_8_gblup_prediction_all_1_1000.rds") +T19_8_gblup_prediction_all_1001_2000=readRDS(file="T19_8_gblup_prediction_all_1001_2000.rds") +T19_8_gblup_prediction_all_2001_3000=readRDS(file="T19_8_gblup_prediction_all_2001_3000.rds") +T19_8_gblup_prediction_all_3001_4000=readRDS(file="T19_8_gblup_prediction_all_3001_4000.rds") +T19_8_gblup_prediction_all_4001_5000=readRDS(file="T19_8_gblup_prediction_all_4001_5000.rds") +T19_8_gblup_prediction_all_5001_6000=readRDS(file="T19_8_gblup_prediction_all_5001_6000.rds") +T19_8_gblup_prediction_all_6001_7297=readRDS(file="T19_8_gblup_prediction_all_6001_7297.rds") +T19_8_gblup_prediction_all=c(T19_8_gblup_prediction_all_1_1000,T19_8_gblup_prediction_all_1001_2000,T19_8_gblup_prediction_all_2001_3000,T19_8_gblup_prediction_all_3001_4000,T19_8_gblup_prediction_all_4001_5000,T19_8_gblup_prediction_all_5001_6000,T19_8_gblup_prediction_all_6001_7297) + +T19_8_gblup_variances_all_1_1000=readRDS(file="T19_8_gblup_variances_all_1_1000.rds") +T19_8_gblup_variances_all_1001_2000=readRDS(file="T19_8_gblup_variances_all_1001_2000.rds") +T19_8_gblup_variances_all_2001_3000=readRDS(file="T19_8_gblup_variances_all_2001_3000.rds") +T19_8_gblup_variances_all_3001_4000=readRDS(file="T19_8_gblup_variances_all_3001_4000.rds") +T19_8_gblup_variances_all_4001_5000=readRDS(file="T19_8_gblup_variances_all_4001_5000.rds") +T19_8_gblup_variances_all_5001_6000=readRDS(file="T19_8_gblup_variances_all_5001_6000.rds") +T19_8_gblup_variances_all_6001_7297=readRDS(file="T19_8_gblup_variances_all_6001_7297.rds") +T19_8_gblup_variances_all=c(T19_8_gblup_variances_all_1_1000,T19_8_gblup_variances_all_1001_2000,T19_8_gblup_variances_all_2001_3000,T19_8_gblup_variances_all_3001_4000,T19_8_gblup_variances_all_4001_5000,T19_8_gblup_variances_all_5001_6000,T19_8_gblup_variances_all_6001_7297) + +saveRDS(T19_8_gblup_prediction_all,"T19_8_gblup_prediction_all.rds") +saveRDS(T19_8_gblup_variances_all,"T19_8_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T19_8_gfblup_prediction_all_1_1000=readRDS(file="T19_8_gfblup_prediction_all_1_1000.rds") +T19_8_gfblup_prediction_all_1001_2000=readRDS(file="T19_8_gfblup_prediction_all_1001_2000.rds") +T19_8_gfblup_prediction_all_2001_3000=readRDS(file="T19_8_gfblup_prediction_all_2001_3000.rds") +T19_8_gfblup_prediction_all_3001_4000=readRDS(file="T19_8_gfblup_prediction_all_3001_4000.rds") +T19_8_gfblup_prediction_all_4001_5000=readRDS(file="T19_8_gfblup_prediction_all_4001_5000.rds") +T19_8_gfblup_prediction_all_5001_6000=readRDS(file="T19_8_gfblup_prediction_all_5001_6000.rds") +T19_8_gfblup_prediction_all_6001_7297=readRDS(file="T19_8_gfblup_prediction_all_6001_7297.rds") + +T19_8_gfblup_variances_all_1_1000=readRDS(file="T19_8_gfblup_variances_all_1_1000.rds") +T19_8_gfblup_variances_all_1001_2000=readRDS(file="T19_8_gfblup_variances_all_1001_2000.rds") +T19_8_gfblup_variances_all_2001_3000=readRDS(file="T19_8_gfblup_variances_all_2001_3000.rds") +T19_8_gfblup_variances_all_3001_4000=readRDS(file="T19_8_gfblup_variances_all_3001_4000.rds") +T19_8_gfblup_variances_all_4001_5000=readRDS(file="T19_8_gfblup_variances_all_4001_5000.rds") +T19_8_gfblup_variances_all_5001_6000=readRDS(file="T19_8_gfblup_variances_all_5001_6000.rds") +T19_8_gfblup_variances_all_6001_7297=readRDS(file="T19_8_gfblup_variances_all_6001_7297.rds") + +cycles=length(T19_8_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T19_8_gfblup_variances_all=rep(list(list()),cycles) +T19_8_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_1_1000[[r]]) + T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_1001_2000[[r]]) + T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_2001_3000[[r]]) + T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_3001_4000[[r]]) + T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_4001_5000[[r]]) + T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_5001_6000[[r]]) + T19_8_gfblup_prediction_all[[r]]<-c(T19_8_gfblup_prediction_all[[r]],T19_8_gfblup_prediction_all_6001_7297[[r]]) + + T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_1_1000[[r]]) + T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_1001_2000[[r]]) + T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_2001_3000[[r]]) + T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_3001_4000[[r]]) + T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_4001_5000[[r]]) + T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_5001_6000[[r]]) + T19_8_gfblup_variances_all[[r]]<-c(T19_8_gfblup_variances_all[[r]],T19_8_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T19_8_gfblup_prediction_all,"T19_8_gfblup_prediction_all.rds") +saveRDS(T19_8_gfblup_variances_all,"T19_8_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T20_1_gblup_prediction_all_1_1000=readRDS(file="T20_1_gblup_prediction_all_1_1000.rds") +T20_1_gblup_prediction_all_1001_2000=readRDS(file="T20_1_gblup_prediction_all_1001_2000.rds") +T20_1_gblup_prediction_all_2001_3000=readRDS(file="T20_1_gblup_prediction_all_2001_3000.rds") +T20_1_gblup_prediction_all_3001_4000=readRDS(file="T20_1_gblup_prediction_all_3001_4000.rds") +T20_1_gblup_prediction_all_4001_5000=readRDS(file="T20_1_gblup_prediction_all_4001_5000.rds") +T20_1_gblup_prediction_all_5001_6000=readRDS(file="T20_1_gblup_prediction_all_5001_6000.rds") +T20_1_gblup_prediction_all_6001_7297=readRDS(file="T20_1_gblup_prediction_all_6001_7297.rds") +T20_1_gblup_prediction_all=c(T20_1_gblup_prediction_all_1_1000,T20_1_gblup_prediction_all_1001_2000,T20_1_gblup_prediction_all_2001_3000,T20_1_gblup_prediction_all_3001_4000,T20_1_gblup_prediction_all_4001_5000,T20_1_gblup_prediction_all_5001_6000,T20_1_gblup_prediction_all_6001_7297) + +T20_1_gblup_variances_all_1_1000=readRDS(file="T20_1_gblup_variances_all_1_1000.rds") +T20_1_gblup_variances_all_1001_2000=readRDS(file="T20_1_gblup_variances_all_1001_2000.rds") +T20_1_gblup_variances_all_2001_3000=readRDS(file="T20_1_gblup_variances_all_2001_3000.rds") +T20_1_gblup_variances_all_3001_4000=readRDS(file="T20_1_gblup_variances_all_3001_4000.rds") +T20_1_gblup_variances_all_4001_5000=readRDS(file="T20_1_gblup_variances_all_4001_5000.rds") +T20_1_gblup_variances_all_5001_6000=readRDS(file="T20_1_gblup_variances_all_5001_6000.rds") +T20_1_gblup_variances_all_6001_7297=readRDS(file="T20_1_gblup_variances_all_6001_7297.rds") +T20_1_gblup_variances_all=c(T20_1_gblup_variances_all_1_1000,T20_1_gblup_variances_all_1001_2000,T20_1_gblup_variances_all_2001_3000,T20_1_gblup_variances_all_3001_4000,T20_1_gblup_variances_all_4001_5000,T20_1_gblup_variances_all_5001_6000,T20_1_gblup_variances_all_6001_7297) + +saveRDS(T20_1_gblup_prediction_all,"T20_1_gblup_prediction_all.rds") +saveRDS(T20_1_gblup_variances_all,"T20_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T20_1_gfblup_prediction_all_1_1000=readRDS(file="T20_1_gfblup_prediction_all_1_1000.rds") +T20_1_gfblup_prediction_all_1001_2000=readRDS(file="T20_1_gfblup_prediction_all_1001_2000.rds") +T20_1_gfblup_prediction_all_2001_3000=readRDS(file="T20_1_gfblup_prediction_all_2001_3000.rds") +T20_1_gfblup_prediction_all_3001_4000=readRDS(file="T20_1_gfblup_prediction_all_3001_4000.rds") +T20_1_gfblup_prediction_all_4001_5000=readRDS(file="T20_1_gfblup_prediction_all_4001_5000.rds") +T20_1_gfblup_prediction_all_5001_6000=readRDS(file="T20_1_gfblup_prediction_all_5001_6000.rds") +T20_1_gfblup_prediction_all_6001_7297=readRDS(file="T20_1_gfblup_prediction_all_6001_7297.rds") + +T20_1_gfblup_variances_all_1_1000=readRDS(file="T20_1_gfblup_variances_all_1_1000.rds") +T20_1_gfblup_variances_all_1001_2000=readRDS(file="T20_1_gfblup_variances_all_1001_2000.rds") +T20_1_gfblup_variances_all_2001_3000=readRDS(file="T20_1_gfblup_variances_all_2001_3000.rds") +T20_1_gfblup_variances_all_3001_4000=readRDS(file="T20_1_gfblup_variances_all_3001_4000.rds") +T20_1_gfblup_variances_all_4001_5000=readRDS(file="T20_1_gfblup_variances_all_4001_5000.rds") +T20_1_gfblup_variances_all_5001_6000=readRDS(file="T20_1_gfblup_variances_all_5001_6000.rds") +T20_1_gfblup_variances_all_6001_7297=readRDS(file="T20_1_gfblup_variances_all_6001_7297.rds") + +cycles=length(T20_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T20_1_gfblup_variances_all=rep(list(list()),cycles) +T20_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_1_1000[[r]]) + T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_1001_2000[[r]]) + T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_2001_3000[[r]]) + T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_3001_4000[[r]]) + T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_4001_5000[[r]]) + T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_5001_6000[[r]]) + T20_1_gfblup_prediction_all[[r]]<-c(T20_1_gfblup_prediction_all[[r]],T20_1_gfblup_prediction_all_6001_7297[[r]]) + + T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_1_1000[[r]]) + T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_1001_2000[[r]]) + T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_2001_3000[[r]]) + T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_3001_4000[[r]]) + T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_4001_5000[[r]]) + T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_5001_6000[[r]]) + T20_1_gfblup_variances_all[[r]]<-c(T20_1_gfblup_variances_all[[r]],T20_1_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T20_1_gfblup_prediction_all,"T20_1_gfblup_prediction_all.rds") +saveRDS(T20_1_gfblup_variances_all,"T20_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T20_2_gblup_prediction_all_1_1000=readRDS(file="T20_2_gblup_prediction_all_1_1000.rds") +T20_2_gblup_prediction_all_1001_2000=readRDS(file="T20_2_gblup_prediction_all_1001_2000.rds") +T20_2_gblup_prediction_all_2001_3000=readRDS(file="T20_2_gblup_prediction_all_2001_3000.rds") +T20_2_gblup_prediction_all_3001_4000=readRDS(file="T20_2_gblup_prediction_all_3001_4000.rds") +T20_2_gblup_prediction_all_4001_5000=readRDS(file="T20_2_gblup_prediction_all_4001_5000.rds") +T20_2_gblup_prediction_all_5001_6000=readRDS(file="T20_2_gblup_prediction_all_5001_6000.rds") +T20_2_gblup_prediction_all_6001_7297=readRDS(file="T20_2_gblup_prediction_all_6001_7297.rds") +T20_2_gblup_prediction_all=c(T20_2_gblup_prediction_all_1_1000,T20_2_gblup_prediction_all_1001_2000,T20_2_gblup_prediction_all_2001_3000,T20_2_gblup_prediction_all_3001_4000,T20_2_gblup_prediction_all_4001_5000,T20_2_gblup_prediction_all_5001_6000,T20_2_gblup_prediction_all_6001_7297) + +T20_2_gblup_variances_all_1_1000=readRDS(file="T20_2_gblup_variances_all_1_1000.rds") +T20_2_gblup_variances_all_1001_2000=readRDS(file="T20_2_gblup_variances_all_1001_2000.rds") +T20_2_gblup_variances_all_2001_3000=readRDS(file="T20_2_gblup_variances_all_2001_3000.rds") +T20_2_gblup_variances_all_3001_4000=readRDS(file="T20_2_gblup_variances_all_3001_4000.rds") +T20_2_gblup_variances_all_4001_5000=readRDS(file="T20_2_gblup_variances_all_4001_5000.rds") +T20_2_gblup_variances_all_5001_6000=readRDS(file="T20_2_gblup_variances_all_5001_6000.rds") +T20_2_gblup_variances_all_6001_7297=readRDS(file="T20_2_gblup_variances_all_6001_7297.rds") +T20_2_gblup_variances_all=c(T20_2_gblup_variances_all_1_1000,T20_2_gblup_variances_all_1001_2000,T20_2_gblup_variances_all_2001_3000,T20_2_gblup_variances_all_3001_4000,T20_2_gblup_variances_all_4001_5000,T20_2_gblup_variances_all_5001_6000,T20_2_gblup_variances_all_6001_7297) + +saveRDS(T20_2_gblup_prediction_all,"T20_2_gblup_prediction_all.rds") +saveRDS(T20_2_gblup_variances_all,"T20_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +T20_2_gfblup_prediction_all_1_1000=readRDS(file="T20_2_gfblup_prediction_all_1_1000.rds") +T20_2_gfblup_prediction_all_1001_2000=readRDS(file="T20_2_gfblup_prediction_all_1001_2000.rds") +T20_2_gfblup_prediction_all_2001_3000=readRDS(file="T20_2_gfblup_prediction_all_2001_3000.rds") +T20_2_gfblup_prediction_all_3001_4000=readRDS(file="T20_2_gfblup_prediction_all_3001_4000.rds") +T20_2_gfblup_prediction_all_4001_5000=readRDS(file="T20_2_gfblup_prediction_all_4001_5000.rds") +T20_2_gfblup_prediction_all_5001_6000=readRDS(file="T20_2_gfblup_prediction_all_5001_6000.rds") +T20_2_gfblup_prediction_all_6001_7297=readRDS(file="T20_2_gfblup_prediction_all_6001_7297.rds") + +T20_2_gfblup_variances_all_1_1000=readRDS(file="T20_2_gfblup_variances_all_1_1000.rds") +T20_2_gfblup_variances_all_1001_2000=readRDS(file="T20_2_gfblup_variances_all_1001_2000.rds") +T20_2_gfblup_variances_all_2001_3000=readRDS(file="T20_2_gfblup_variances_all_2001_3000.rds") +T20_2_gfblup_variances_all_3001_4000=readRDS(file="T20_2_gfblup_variances_all_3001_4000.rds") +T20_2_gfblup_variances_all_4001_5000=readRDS(file="T20_2_gfblup_variances_all_4001_5000.rds") +T20_2_gfblup_variances_all_5001_6000=readRDS(file="T20_2_gfblup_variances_all_5001_6000.rds") +T20_2_gfblup_variances_all_6001_7297=readRDS(file="T20_2_gfblup_variances_all_6001_7297.rds") + +cycles=length(T20_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +T20_2_gfblup_variances_all=rep(list(list()),cycles) +T20_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_1_1000[[r]]) + T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_1001_2000[[r]]) + T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_2001_3000[[r]]) + T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_3001_4000[[r]]) + T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_4001_5000[[r]]) + T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_5001_6000[[r]]) + T20_2_gfblup_prediction_all[[r]]<-c(T20_2_gfblup_prediction_all[[r]],T20_2_gfblup_prediction_all_6001_7297[[r]]) + + T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_1_1000[[r]]) + T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_1001_2000[[r]]) + T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_2001_3000[[r]]) + T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_3001_4000[[r]]) + T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_4001_5000[[r]]) + T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_5001_6000[[r]]) + T20_2_gfblup_variances_all[[r]]<-c(T20_2_gfblup_variances_all[[r]],T20_2_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(T20_2_gfblup_prediction_all,"T20_2_gfblup_prediction_all.rds") +saveRDS(T20_2_gfblup_variances_all,"T20_2_gfblup_variances_all.rds") + diff --git a/code/using_GO/pla/T14_1_1001_2000.R b/code/using_GO/pla/T14_1_1001_2000.R index 5e317bd1e8e751b9c66b3f9362ae00e1ab18722a..76efe84b63609d61c223fe5879a9e4588c623e8d 100644 --- a/code/using_GO/pla/T14_1_1001_2000.R +++ b/code/using_GO/pla/T14_1_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1001:2000] rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_1_1_1000.R b/code/using_GO/pla/T14_1_1_1000.R index 9516a0f7de3a414c67888e923b42aded00a359b5..403c8bda7af1f62ed8d929a04187b0206bf8c9cd 100644 --- a/code/using_GO/pla/T14_1_1_1000.R +++ b/code/using_GO/pla/T14_1_1_1000.R @@ -7,9 +7,25 @@ is.installed <- function(mypkg) is.element(mypkg, installed.packages()[,1]) } ######################################################################################## +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") - +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ # install.packages("backports") @@ -32,26 +48,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +78,7 @@ GF_filtered<-GF_filtered[1:1000] rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") +gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_1_2001_3000.R b/code/using_GO/pla/T14_1_2001_3000.R index 231392187c2aea5bb7de4fee173eb0886c3cd31d..e2b687470063e04375f45b9ff78f65ad5bce81f0 100644 --- a/code/using_GO/pla/T14_1_2001_3000.R +++ b/code/using_GO/pla/T14_1_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[2001:3000] rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_1_3001_4000.R b/code/using_GO/pla/T14_1_3001_4000.R index 8ac39a53f616ad79e6a466ff6e7790f51ddc12bd..9a405894cd9908e8114ec8a3f7b900032855f489 100644 --- a/code/using_GO/pla/T14_1_3001_4000.R +++ b/code/using_GO/pla/T14_1_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[3001:4000] rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_1_4001_5000.R b/code/using_GO/pla/T14_1_4001_5000.R index 3e47124948810f85cc972080f42f731cd9392e20..81ca77f14cd05fbcf7875343d18470c39796b2d9 100644 --- a/code/using_GO/pla/T14_1_4001_5000.R +++ b/code/using_GO/pla/T14_1_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[4001:5000] rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_1_5001_6000.R b/code/using_GO/pla/T14_1_5001_6000.R index eeed787694c5a9c1af6c6da1cd7964ad96fc9a80..4c4debc437f588b22c06c67d5165d73b69baa0c1 100644 --- a/code/using_GO/pla/T14_1_5001_6000.R +++ b/code/using_GO/pla/T14_1_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[5001:6000] rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_1_6001_7297.R b/code/using_GO/pla/T14_1_6001_7297.R index 7697a444ca12d379b5f24b2793952f3ceeeaf190..b00fe794c4c02401d8c71aa57c79d04f21f75e99 100644 --- a/code/using_GO/pla/T14_1_6001_7297.R +++ b/code/using_GO/pla/T14_1_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[6001:7297] rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_2_1001_2000.R b/code/using_GO/pla/T14_2_1001_2000.R index 5a11ab6c4163a34cd81face106bb9f82ee38b449..fc02a47047030e4033a0f521ce590dc8b8831728 100644 --- a/code/using_GO/pla/T14_2_1001_2000.R +++ b/code/using_GO/pla/T14_2_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1001:2000] rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_2_1_1000.R b/code/using_GO/pla/T14_2_1_1000.R index e4d1021615955b54b48e1140e0c63a4d2c49a3ee..be9ef7e191abb3ada3eaed7d5d4e37a52bd7ee5c 100644 --- a/code/using_GO/pla/T14_2_1_1000.R +++ b/code/using_GO/pla/T14_2_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1:1000] rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_2_2001_3000.R b/code/using_GO/pla/T14_2_2001_3000.R index f1414c60269b04d021616f371c2c5f6cf8acd2dd..74c9f92093f4a9e8804fa65d24baabb184069354 100644 --- a/code/using_GO/pla/T14_2_2001_3000.R +++ b/code/using_GO/pla/T14_2_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[2001:3000] rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_2_3001_4000.R b/code/using_GO/pla/T14_2_3001_4000.R index ae553eab07c0bef1cab09b35017edd504da3f868..0ad0b08f1b75f2d1bb7bcab5fa4763b14d5eeabf 100644 --- a/code/using_GO/pla/T14_2_3001_4000.R +++ b/code/using_GO/pla/T14_2_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[3001:4000] rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_2_4001_5000.R b/code/using_GO/pla/T14_2_4001_5000.R index 97de7ee28e7ecb75ef40973130b96e7e00cadd99..331d3c97ebfb802b095ea08048b56b688f7a94e7 100644 --- a/code/using_GO/pla/T14_2_4001_5000.R +++ b/code/using_GO/pla/T14_2_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[4001:5000] rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_2_5001_6000.R b/code/using_GO/pla/T14_2_5001_6000.R index fc380291e002715f3b0001e626ed067694a4a68b..118bdf25d867ad592b5f34bb52c91beb25c1f7a8 100644 --- a/code/using_GO/pla/T14_2_5001_6000.R +++ b/code/using_GO/pla/T14_2_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[5001:6000] rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_2_6001_7297.R b/code/using_GO/pla/T14_2_6001_7297.R index 1e2fb34f65dc4aee1ab10b454815a2fde0768ab3..23065af55e25b29b73e0629b78a24ab751dbe487 100644 --- a/code/using_GO/pla/T14_2_6001_7297.R +++ b/code/using_GO/pla/T14_2_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[6001:7297] rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_3_1001_2000.R b/code/using_GO/pla/T14_3_1001_2000.R index d39f3ac47875915eece7cd25925cdd5099133fa9..f323f91bf7e46993427a65d9979e62500dc2a8cb 100644 --- a/code/using_GO/pla/T14_3_1001_2000.R +++ b/code/using_GO/pla/T14_3_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1001:2000] rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_3_1_1000.R b/code/using_GO/pla/T14_3_1_1000.R index e88f5c0b67e367173fc5a64d3edd1fa69b7a59f4..4a66d7366731011e01817c556c891a13d4ae51e0 100644 --- a/code/using_GO/pla/T14_3_1_1000.R +++ b/code/using_GO/pla/T14_3_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1:1000] rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_3_2001_3000.R b/code/using_GO/pla/T14_3_2001_3000.R index 151fff055f9d65278c5bfd22ca66286525d547dc..8711683a066e6243d77bee5d28fdbd80a7e00bbc 100644 --- a/code/using_GO/pla/T14_3_2001_3000.R +++ b/code/using_GO/pla/T14_3_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[2001:3000] rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_3_3001_4000.R b/code/using_GO/pla/T14_3_3001_4000.R index 8cc719c3562f96124f0eef40b88a56bcaa9bb8b2..93b77d967163da9510316c8902dde88c0de983bd 100644 --- a/code/using_GO/pla/T14_3_3001_4000.R +++ b/code/using_GO/pla/T14_3_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[3001:4000] rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_3_4001_5000.R b/code/using_GO/pla/T14_3_4001_5000.R index 7100d155e486e572b13af3d32b533dabbab51d91..4a3730876f0dda540dec75c4ce53f83546ed5543 100644 --- a/code/using_GO/pla/T14_3_4001_5000.R +++ b/code/using_GO/pla/T14_3_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[4001:5000] rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_3_5001_6000.R b/code/using_GO/pla/T14_3_5001_6000.R index 26e941c439b12d9b187a4e46cd70301f335c60b3..233ff2190a89a1f049936388804cf85d00b94f67 100644 --- a/code/using_GO/pla/T14_3_5001_6000.R +++ b/code/using_GO/pla/T14_3_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[5001:6000] rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_3_6001_7297.R b/code/using_GO/pla/T14_3_6001_7297.R index 9130398b04e5a297e0e06e3adde115a31dea735f..4b4c77e77058db8f5c92b26876809ee55b6777cf 100644 --- a/code/using_GO/pla/T14_3_6001_7297.R +++ b/code/using_GO/pla/T14_3_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[6001:7297] rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_4_1001_2000.R b/code/using_GO/pla/T14_4_1001_2000.R index 3e4419da67531bf122954302ce2ea980277503e6..4168ad3611f347fb0c03878d684a456f35ca0bd2 100644 --- a/code/using_GO/pla/T14_4_1001_2000.R +++ b/code/using_GO/pla/T14_4_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1001:2000] rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_4_1_1000.R b/code/using_GO/pla/T14_4_1_1000.R index fb82682437af2202908cadc561225beff16b6073..dcd8e925a93239abff52163787ba087c02d5fd0b 100644 --- a/code/using_GO/pla/T14_4_1_1000.R +++ b/code/using_GO/pla/T14_4_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1:1000] rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_4_2001_3000.R b/code/using_GO/pla/T14_4_2001_3000.R index 6bd2e0b6bb7e2196c2ed4b0391970764879aab02..7af88f51cc977924987d4d52a9ab3cb46781be54 100644 --- a/code/using_GO/pla/T14_4_2001_3000.R +++ b/code/using_GO/pla/T14_4_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[2001:3000] rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_4_3001_4000.R b/code/using_GO/pla/T14_4_3001_4000.R index 7ab760583879dca70dccb70ef4c5e5125cc9d33f..2e82b0a0592923f4810a7951ccbcdceea61e6e3f 100644 --- a/code/using_GO/pla/T14_4_3001_4000.R +++ b/code/using_GO/pla/T14_4_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[3001:4000] rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_4_4001_5000.R b/code/using_GO/pla/T14_4_4001_5000.R index 5a05ccbea0c20ed31c39514cc0f9c5e4be1cf5f5..d81659e7cd3ff1d3447ff8d9a33b9b52d8c619f1 100644 --- a/code/using_GO/pla/T14_4_4001_5000.R +++ b/code/using_GO/pla/T14_4_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[4001:5000] rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_4_5001_6000.R b/code/using_GO/pla/T14_4_5001_6000.R index 8a992cf578a32d1135af92dde20feeb67a6e44de..a493ada8ede30e299879a3bb37fba187d342ab74 100644 --- a/code/using_GO/pla/T14_4_5001_6000.R +++ b/code/using_GO/pla/T14_4_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[5001:6000] rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_4_6001_7297.R b/code/using_GO/pla/T14_4_6001_7297.R index 0c0e0e5bd1d532954073512b4cd4a1acb89f760c..4fd17e21624401e28f5eac54ae1a2ac8ee29587f 100644 --- a/code/using_GO/pla/T14_4_6001_7297.R +++ b/code/using_GO/pla/T14_4_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[6001:7297] rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_5_1001_2000.R b/code/using_GO/pla/T14_5_1001_2000.R index 6f75e58dd65429aa8858e4d508045d500324bd48..3b71ca4ed75d2ca29324ef32a1ff8842555604bf 100644 --- a/code/using_GO/pla/T14_5_1001_2000.R +++ b/code/using_GO/pla/T14_5_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1001:2000] rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_5_1_1000.R b/code/using_GO/pla/T14_5_1_1000.R index 61189576089e82f720b5df5220d55861e72749c7..214e6c37e0227747dc6dd6f8fe7867473bba06ed 100644 --- a/code/using_GO/pla/T14_5_1_1000.R +++ b/code/using_GO/pla/T14_5_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1:1000] rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_5_2001_3000.R b/code/using_GO/pla/T14_5_2001_3000.R index a5b43288f4d2d2c9ee577cc6c9be4332483ecbb2..2239b920cd4f3ca904e978793fe19b3790ad3c70 100644 --- a/code/using_GO/pla/T14_5_2001_3000.R +++ b/code/using_GO/pla/T14_5_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[2001:3000] rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_5_3001_4000.R b/code/using_GO/pla/T14_5_3001_4000.R index 87343d18dbaa1d2a09e49fb108be8f89d6e71951..fca111efe6abac2fcd3bb23a656075c8d6792c51 100644 --- a/code/using_GO/pla/T14_5_3001_4000.R +++ b/code/using_GO/pla/T14_5_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[3001:4000] rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_5_4001_5000.R b/code/using_GO/pla/T14_5_4001_5000.R index a43c6dbb04471baa8fef2b78cd279be0020d44d0..eb00f67013d148a24b898367c1ab54faf268045a 100644 --- a/code/using_GO/pla/T14_5_4001_5000.R +++ b/code/using_GO/pla/T14_5_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[4001:5000] rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_5_5001_6000.R b/code/using_GO/pla/T14_5_5001_6000.R index d6df8951a6b01a39ccc4ce7869c0828d326af3a1..7de58644ece973b4ad45330d2eb5d6d58cf20286 100644 --- a/code/using_GO/pla/T14_5_5001_6000.R +++ b/code/using_GO/pla/T14_5_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[5001:6000] rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_5_6001_7297.R b/code/using_GO/pla/T14_5_6001_7297.R index 43081415ad495fb04830106caba96cf7f9e3967a..a0d795698fbe60e9b4a5b743498c32e952596e17 100644 --- a/code/using_GO/pla/T14_5_6001_7297.R +++ b/code/using_GO/pla/T14_5_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[6001:7297] rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_6_1001_2000.R b/code/using_GO/pla/T14_6_1001_2000.R index 615caa4c37d841cd10ac7212aceef64b0047bb33..86e67e3eefc19a14ad8e8aec29c79585bc736c3c 100644 --- a/code/using_GO/pla/T14_6_1001_2000.R +++ b/code/using_GO/pla/T14_6_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1001:2000] rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_6_1_1000.R b/code/using_GO/pla/T14_6_1_1000.R index 49aa03e097389e9d28c7cd63695cc5dfd0a98233..3b1a8c1454cf2a317ccd9fcf6557a11996cbdefc 100644 --- a/code/using_GO/pla/T14_6_1_1000.R +++ b/code/using_GO/pla/T14_6_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1:1000] rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_6_2001_3000.R b/code/using_GO/pla/T14_6_2001_3000.R index c6cbc4c2f092927d9cddc46bfae3041b020d3bcb..45c9f76d2f959ef8a46447c1a2949a45874a51ae 100644 --- a/code/using_GO/pla/T14_6_2001_3000.R +++ b/code/using_GO/pla/T14_6_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[2001:3000] rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_6_3001_4000.R b/code/using_GO/pla/T14_6_3001_4000.R index 6fa0004adef89de829fac2c71fa2182f0c65c2b2..53208cadce90acc95743bca98cd47f38825d5791 100644 --- a/code/using_GO/pla/T14_6_3001_4000.R +++ b/code/using_GO/pla/T14_6_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[3001:4000] rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_6_4001_5000.R b/code/using_GO/pla/T14_6_4001_5000.R index 5ff2b569bc4e31a85ddebd5d2a1936aa37a899dc..1c2b54eb87088747fab51fbd7dbff147de052bff 100644 --- a/code/using_GO/pla/T14_6_4001_5000.R +++ b/code/using_GO/pla/T14_6_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[4001:5000] rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_6_5001_6000.R b/code/using_GO/pla/T14_6_5001_6000.R index e9bc5e08a29d5b87419786d9668cebe24813dfab..d9d2f5dc40f2c361aae01594c3688f5545600884 100644 --- a/code/using_GO/pla/T14_6_5001_6000.R +++ b/code/using_GO/pla/T14_6_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[5001:6000] rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_6_6001_7297.R b/code/using_GO/pla/T14_6_6001_7297.R index c3c71cc3cc259707dbc0b93d77475f94f22ed272..9f23b4e806bc26e57cdda5fbfaeebc5259138173 100644 --- a/code/using_GO/pla/T14_6_6001_7297.R +++ b/code/using_GO/pla/T14_6_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[6001:7297] rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_7_1001_2000.R b/code/using_GO/pla/T14_7_1001_2000.R index fb02a3aae488769455d384beede1a927a2df812f..c6341978442e470f118e19a9e02d77581a441e3d 100644 --- a/code/using_GO/pla/T14_7_1001_2000.R +++ b/code/using_GO/pla/T14_7_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1001:2000] rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_7_1_1000.R b/code/using_GO/pla/T14_7_1_1000.R index 56d9307e51aa3fe2065725760005c5d5ace1a5e9..3544e74bbea7c24373e6e8925958b65cf251d544 100644 --- a/code/using_GO/pla/T14_7_1_1000.R +++ b/code/using_GO/pla/T14_7_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1:1000] rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_7_2001_3000.R b/code/using_GO/pla/T14_7_2001_3000.R index ec3844ffe386cc6ccf952406dd96d0ca6c82dbc0..73c0600423fae7c4c4ee1f8ba0bfe3b34896cdb5 100644 --- a/code/using_GO/pla/T14_7_2001_3000.R +++ b/code/using_GO/pla/T14_7_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[2001:3000] rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_7_3001_4000.R b/code/using_GO/pla/T14_7_3001_4000.R index 59ca235e6bff3d87006908c070f4e39135c89bf6..a3de9fbc46b14d987366f59bdd3373df1618a4cd 100644 --- a/code/using_GO/pla/T14_7_3001_4000.R +++ b/code/using_GO/pla/T14_7_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[3001:4000] rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_7_4001_5000.R b/code/using_GO/pla/T14_7_4001_5000.R index a9742f2cba1db8a960a5c23c1998c82d62c870d6..975a04f7e53e8b0fc03c58020d2fa9623adb84c1 100644 --- a/code/using_GO/pla/T14_7_4001_5000.R +++ b/code/using_GO/pla/T14_7_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[4001:5000] rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_7_5001_6000.R b/code/using_GO/pla/T14_7_5001_6000.R index 2a794aaad3490c54908cca89dad88b43c47ea20b..d25c511035bf58a9734984b1df07c2195f29ca52 100644 --- a/code/using_GO/pla/T14_7_5001_6000.R +++ b/code/using_GO/pla/T14_7_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[5001:6000] rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_7_6001_7297.R b/code/using_GO/pla/T14_7_6001_7297.R index 378da97ccd638196f31636d382c60a6e77ca988d..3a3a18de0a3c6fe3b9731d3c7b7f628a6e64eebe 100644 --- a/code/using_GO/pla/T14_7_6001_7297.R +++ b/code/using_GO/pla/T14_7_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[6001:7297] rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_8_1001_2000.R b/code/using_GO/pla/T14_8_1001_2000.R index 2b248378bf3588b08fc739a78504e1504cfd6b55..bbfb37e268b5b38d267760228a536ebe9440c642 100644 --- a/code/using_GO/pla/T14_8_1001_2000.R +++ b/code/using_GO/pla/T14_8_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1001:2000] rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_8_1_1000.R b/code/using_GO/pla/T14_8_1_1000.R index 7c10b96bb1c9a8d736babf7dae01182ab3bb39a1..71896ade3e9dda875baa0def36fd1c34bcd00f34 100644 --- a/code/using_GO/pla/T14_8_1_1000.R +++ b/code/using_GO/pla/T14_8_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[1:1000] rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_8_2001_3000.R b/code/using_GO/pla/T14_8_2001_3000.R index 723ac35e11a964a74b8d4488e6975d16626295fc..ea91644d31418d51bfb323685da7d6fadea9d592 100644 --- a/code/using_GO/pla/T14_8_2001_3000.R +++ b/code/using_GO/pla/T14_8_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[2001:3000] rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_8_3001_4000.R b/code/using_GO/pla/T14_8_3001_4000.R index 5d2d962e90a0f7340111b1a6feb828260207f5d4..85697e5c6696c554841d2e2b8cd5e3fabcc752a3 100644 --- a/code/using_GO/pla/T14_8_3001_4000.R +++ b/code/using_GO/pla/T14_8_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[3001:4000] rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_8_4001_5000.R b/code/using_GO/pla/T14_8_4001_5000.R index 000023127afae0ef854df9719f1ebcd1741fbc8d..9be86c0e48ea6e81ce462dab02ec8e5c38e797f4 100644 --- a/code/using_GO/pla/T14_8_4001_5000.R +++ b/code/using_GO/pla/T14_8_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[4001:5000] rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_8_5001_6000.R b/code/using_GO/pla/T14_8_5001_6000.R index ff599fc4b7f09ff251b5870f8b482631f55e1367..16f0677ff869049b9457d895ea081cc24f407ae0 100644 --- a/code/using_GO/pla/T14_8_5001_6000.R +++ b/code/using_GO/pla/T14_8_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[5001:6000] rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T14_8_6001_7297.R b/code/using_GO/pla/T14_8_6001_7297.R index 3a0790d2c95ffbf868f6e7f95ed421aa0ec68587..98dabdfc7adbfb4ced36680064973df3baa0c4da 100644 --- a/code/using_GO/pla/T14_8_6001_7297.R +++ b/code/using_GO/pla/T14_8_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -62,7 +80,7 @@ GF_filtered<-GF_filtered[6001:7297] rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T14_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_1_1001_2000.R b/code/using_GO/pla/T15_1_1001_2000.R index 39066777dded5a36f535d8c198a3b35254c82d20..79d3f61dd6cdd923b076427040d9a452f1fe0924 100644 --- a/code/using_GO/pla/T15_1_1001_2000.R +++ b/code/using_GO/pla/T15_1_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_1_1_1000.R b/code/using_GO/pla/T15_1_1_1000.R index 461709bb078b19b4e99e2a05f5055281f946c4af..96fa54a59397911f0a2dd308a298ddece70b0906 100644 --- a/code/using_GO/pla/T15_1_1_1000.R +++ b/code/using_GO/pla/T15_1_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_1_2001_3000.R b/code/using_GO/pla/T15_1_2001_3000.R index ef4eac42a690dcc2e735ea7047d5a98e9cb9f120..7eb18f52e9eac37b0653233dcf2550e613bca359 100644 --- a/code/using_GO/pla/T15_1_2001_3000.R +++ b/code/using_GO/pla/T15_1_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_1_3001_4000.R b/code/using_GO/pla/T15_1_3001_4000.R index 3a101f1d0a9fd4f60bd034570f65e6be9be24038..73535a67fbc48d9b035634870e4093c7bcf55d20 100644 --- a/code/using_GO/pla/T15_1_3001_4000.R +++ b/code/using_GO/pla/T15_1_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_1_4001_5000.R b/code/using_GO/pla/T15_1_4001_5000.R index 8258197e4e77441eca0d54dd162ead377d37e93d..10ca074909717a6301b4e576de6046a6f3b1879d 100644 --- a/code/using_GO/pla/T15_1_4001_5000.R +++ b/code/using_GO/pla/T15_1_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_1_5001_6000.R b/code/using_GO/pla/T15_1_5001_6000.R index d5998cfd5d5c2ce3566b9417b43933847e96e794..2b0d451597b6d14be8b2ebb4979090aa5d9dafdd 100644 --- a/code/using_GO/pla/T15_1_5001_6000.R +++ b/code/using_GO/pla/T15_1_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_1_6001_7297.R b/code/using_GO/pla/T15_1_6001_7297.R index 27cae6a4f8d7fd42d5ef95c8cd3c26a5d8afd939..dfe215ad239d878b1fa12e79b2cd2aeb076c173a 100644 --- a/code/using_GO/pla/T15_1_6001_7297.R +++ b/code/using_GO/pla/T15_1_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_2_1001_2000.R b/code/using_GO/pla/T15_2_1001_2000.R index 708769f34a4d7475092a8ae6730c52a92872c1a9..71dd7c7668e69de1f83b16e99138c625a353ed31 100644 --- a/code/using_GO/pla/T15_2_1001_2000.R +++ b/code/using_GO/pla/T15_2_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_2_1_1000.R b/code/using_GO/pla/T15_2_1_1000.R index 05caeebbd7b27a9c2726900bd0680ffef4ca35a1..d321b2b4517f8c8fed436977f955c2aee931737e 100644 --- a/code/using_GO/pla/T15_2_1_1000.R +++ b/code/using_GO/pla/T15_2_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_2_2001_3000.R b/code/using_GO/pla/T15_2_2001_3000.R index defc89944050f3ff62478d598a6a19acfaa7d45d..234cf0843c0a02a10daf308bd857610f76f782c2 100644 --- a/code/using_GO/pla/T15_2_2001_3000.R +++ b/code/using_GO/pla/T15_2_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_2_3001_4000.R b/code/using_GO/pla/T15_2_3001_4000.R index 4eac70cf215cd3a32c0d5fd6384d519ac7f78719..18bcb38b898ec3047f1f7ce8bc3f6b2157f9cf56 100644 --- a/code/using_GO/pla/T15_2_3001_4000.R +++ b/code/using_GO/pla/T15_2_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_2_4001_5000.R b/code/using_GO/pla/T15_2_4001_5000.R index fbac682d365b3245988e5dff7428e42c48f87e0d..ed9f2087affecfccc42c41d8e1bce3449133317d 100644 --- a/code/using_GO/pla/T15_2_4001_5000.R +++ b/code/using_GO/pla/T15_2_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_2_5001_6000.R b/code/using_GO/pla/T15_2_5001_6000.R index 37ee8d403e63fbf1553443d751fef570433a2957..452ba5c04252e6424a45d8ceeae60e691ee2847a 100644 --- a/code/using_GO/pla/T15_2_5001_6000.R +++ b/code/using_GO/pla/T15_2_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_2_6001_7297.R b/code/using_GO/pla/T15_2_6001_7297.R index 036845f5ead31c5319ee47db47f73032bb0f1dde..6337c5c2312b8d4fff67e6b757930ac44fae31a6 100644 --- a/code/using_GO/pla/T15_2_6001_7297.R +++ b/code/using_GO/pla/T15_2_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_3_1001_2000.R b/code/using_GO/pla/T15_3_1001_2000.R index 022bfccf5e4a6e4bcbb78c0f2c5c9eb3ae2753c1..0df2773d53d5ce1079e70b170d95129c85fe539d 100644 --- a/code/using_GO/pla/T15_3_1001_2000.R +++ b/code/using_GO/pla/T15_3_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_3_1_1000.R b/code/using_GO/pla/T15_3_1_1000.R index 28741e3f334cedc041242be463e56baea005544f..21bd8eef36481900e71ff66d98a401804aa9213b 100644 --- a/code/using_GO/pla/T15_3_1_1000.R +++ b/code/using_GO/pla/T15_3_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_3_2001_3000.R b/code/using_GO/pla/T15_3_2001_3000.R index 06b102d5dab10e0f8c172a0dd21c90446dbd1e63..e3aba60994deb59a00123c783068aaf7a2b08a4c 100644 --- a/code/using_GO/pla/T15_3_2001_3000.R +++ b/code/using_GO/pla/T15_3_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_3_3001_4000.R b/code/using_GO/pla/T15_3_3001_4000.R index 24a12e53a1e9ed21ad24ed9676386824c2f71e3d..71e8c19550ed7a820ff18016b36c5c38613fa6ed 100644 --- a/code/using_GO/pla/T15_3_3001_4000.R +++ b/code/using_GO/pla/T15_3_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_3_4001_5000.R b/code/using_GO/pla/T15_3_4001_5000.R index ab79059eebe8705c29852e7cc7d0a9c8b6cdd421..9a4110ee06d8f190dfa18b2610dcbad60c2bd64e 100644 --- a/code/using_GO/pla/T15_3_4001_5000.R +++ b/code/using_GO/pla/T15_3_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_3_5001_6000.R b/code/using_GO/pla/T15_3_5001_6000.R index 40ca42f2d79926656b932cc0bfc01a9e57bd93aa..ca08ede37e1a71b9dfaf576ed2325498ce39c866 100644 --- a/code/using_GO/pla/T15_3_5001_6000.R +++ b/code/using_GO/pla/T15_3_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_3_6001_7297.R b/code/using_GO/pla/T15_3_6001_7297.R index b9945bc0bf7005d4d2112c2b8e048de596216dca..d1b50dd6fe03a40ad1ab70ae62dc6f03942b07a1 100644 --- a/code/using_GO/pla/T15_3_6001_7297.R +++ b/code/using_GO/pla/T15_3_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_4_1001_2000.R b/code/using_GO/pla/T15_4_1001_2000.R index 2b4d312fea5e0267b044a7df30dd202307e47966..78002b6835ce2b717b3081cef571cd0cde197d17 100644 --- a/code/using_GO/pla/T15_4_1001_2000.R +++ b/code/using_GO/pla/T15_4_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_4_1_1000.R b/code/using_GO/pla/T15_4_1_1000.R index 056cb6baaae5c119f25d8db3109afcae27317414..cfa5af276c1c4e416c676512e0adfcfc06283658 100644 --- a/code/using_GO/pla/T15_4_1_1000.R +++ b/code/using_GO/pla/T15_4_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_4_2001_3000.R b/code/using_GO/pla/T15_4_2001_3000.R index 8e4e371b371a07bdd3aa66e6487f7f01debad932..1e244f2a1c7353c9a7606603f81db6da598f1030 100644 --- a/code/using_GO/pla/T15_4_2001_3000.R +++ b/code/using_GO/pla/T15_4_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_4_3001_4000.R b/code/using_GO/pla/T15_4_3001_4000.R index 21bb254968025c8612e2f389df283c5c7313d6cf..d55b5cd7e91f1dc26f4e8da3467924bfbe1678cd 100644 --- a/code/using_GO/pla/T15_4_3001_4000.R +++ b/code/using_GO/pla/T15_4_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_4_4001_5000.R b/code/using_GO/pla/T15_4_4001_5000.R index 37fedac900e6bfeee13e3c6590469694f2eb396e..532b14f3af20e7f9f2744406b48d5e4713248ffd 100644 --- a/code/using_GO/pla/T15_4_4001_5000.R +++ b/code/using_GO/pla/T15_4_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_4_5001_6000.R b/code/using_GO/pla/T15_4_5001_6000.R index 5c474ab1ef70f1bda21c3924d7f04df6b62a98c1..e8957c627628db36b542a30e6e62813f7625cf03 100644 --- a/code/using_GO/pla/T15_4_5001_6000.R +++ b/code/using_GO/pla/T15_4_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_4_6001_7297.R b/code/using_GO/pla/T15_4_6001_7297.R index 6b4e58e333e038727e2542acabeba14bc1eba34c..d9018c370b2ba03357ff0e603da25a3f6857bba5 100644 --- a/code/using_GO/pla/T15_4_6001_7297.R +++ b/code/using_GO/pla/T15_4_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_5_1001_2000.R b/code/using_GO/pla/T15_5_1001_2000.R index f2ffdac3ecde5de2d6fb2c2d7a73627963c8b401..db47e64f73b8d51365c6da05306376cee0b5d27b 100644 --- a/code/using_GO/pla/T15_5_1001_2000.R +++ b/code/using_GO/pla/T15_5_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_5_1_1000.R b/code/using_GO/pla/T15_5_1_1000.R index 566bf793b50a925c90646d481fded38fda28f29e..3d637b368acad3a2634f48a37267d1540fa8745c 100644 --- a/code/using_GO/pla/T15_5_1_1000.R +++ b/code/using_GO/pla/T15_5_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_5_2001_3000.R b/code/using_GO/pla/T15_5_2001_3000.R index d7f1909218a059bcac017150ceead726526ca0d3..c20aa254bc7b0bdb04953836341f73b9fb896cd6 100644 --- a/code/using_GO/pla/T15_5_2001_3000.R +++ b/code/using_GO/pla/T15_5_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_5_3001_4000.R b/code/using_GO/pla/T15_5_3001_4000.R index c4dc6480e6da82736a17bfe599761444cc8335c8..b0311167cd9519e46ecd3159b07992a2d05355f2 100644 --- a/code/using_GO/pla/T15_5_3001_4000.R +++ b/code/using_GO/pla/T15_5_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_5_4001_5000.R b/code/using_GO/pla/T15_5_4001_5000.R index 949ffc13cb427880e415a86f20e3944ffd31de19..c7472df63019ba28c2ca40740d40097a1eadef04 100644 --- a/code/using_GO/pla/T15_5_4001_5000.R +++ b/code/using_GO/pla/T15_5_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_5_5001_6000.R b/code/using_GO/pla/T15_5_5001_6000.R index 49e9a78765754793557e6a7bfe9dee2826419faf..8a8f8a59875b79d15f920d391f8d473d83b8d098 100644 --- a/code/using_GO/pla/T15_5_5001_6000.R +++ b/code/using_GO/pla/T15_5_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_5_6001_7297.R b/code/using_GO/pla/T15_5_6001_7297.R index e93c701367c6b84389979f62dd2274818d917dae..1fa2d54187f0d8e150ad8bce768c53bbd2131d0a 100644 --- a/code/using_GO/pla/T15_5_6001_7297.R +++ b/code/using_GO/pla/T15_5_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_6_1001_2000.R b/code/using_GO/pla/T15_6_1001_2000.R index 6e615e7b24918bbdbf493ca780f7abbad24f8adc..b1a51a09df5d759f58adc296821c7c37f6be53a1 100644 --- a/code/using_GO/pla/T15_6_1001_2000.R +++ b/code/using_GO/pla/T15_6_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_6_1_1000.R b/code/using_GO/pla/T15_6_1_1000.R index c302bb2f66b059a531e30ec24b9f6780594529d2..85b8efcaacc66d8289f8bdba0ab1b5417eab339a 100644 --- a/code/using_GO/pla/T15_6_1_1000.R +++ b/code/using_GO/pla/T15_6_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_6_2001_3000.R b/code/using_GO/pla/T15_6_2001_3000.R index 36197e0d6d430137b6ede8061a7470cc55b5781c..c5b57bd568b7b8c480c90e4764a86a8e3df413a5 100644 --- a/code/using_GO/pla/T15_6_2001_3000.R +++ b/code/using_GO/pla/T15_6_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_6_3001_4000.R b/code/using_GO/pla/T15_6_3001_4000.R index 42c18753da3f9bb196cd400e25c380ebb02b18cd..446cb3fd1618e2fefbb2d865af26d2a14587f3e3 100644 --- a/code/using_GO/pla/T15_6_3001_4000.R +++ b/code/using_GO/pla/T15_6_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_6_4001_5000.R b/code/using_GO/pla/T15_6_4001_5000.R index 760db500d36667d0b0bee817708f1cf16b258399..5d4ed085c80c0f851602dbcac29de375e4b9d63e 100644 --- a/code/using_GO/pla/T15_6_4001_5000.R +++ b/code/using_GO/pla/T15_6_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_6_5001_6000.R b/code/using_GO/pla/T15_6_5001_6000.R index b23f2accc26da8c33c7ded1b30bb76bee8a1b512..5114d926f6f873074118e7854fc87737796a8519 100644 --- a/code/using_GO/pla/T15_6_5001_6000.R +++ b/code/using_GO/pla/T15_6_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_6_6001_7297.R b/code/using_GO/pla/T15_6_6001_7297.R index 78c2aeee77540b6ec412dd959a562380c94e7c2d..96e8c78bd51b8c7f64056b42a25ae91a889c21e0 100644 --- a/code/using_GO/pla/T15_6_6001_7297.R +++ b/code/using_GO/pla/T15_6_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_7_1001_2000.R b/code/using_GO/pla/T15_7_1001_2000.R index c0786b9fb272d6e67aee3fcfb40919d03e0cfa08..2a39ba210733ab021a6893634f7c1aa8f1498a19 100644 --- a/code/using_GO/pla/T15_7_1001_2000.R +++ b/code/using_GO/pla/T15_7_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_7_1_1000.R b/code/using_GO/pla/T15_7_1_1000.R index 86ba4bcdc9c443d548dbc92853d50e09aafdb0cf..79d628a3d82e9e97e483438712f01c7a3f0c5a27 100644 --- a/code/using_GO/pla/T15_7_1_1000.R +++ b/code/using_GO/pla/T15_7_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_7_2001_3000.R b/code/using_GO/pla/T15_7_2001_3000.R index 4c7d97704efba722eccf37e10e01eacab50f6961..4655addce931a1de8f07abb15d806a7aa65fc845 100644 --- a/code/using_GO/pla/T15_7_2001_3000.R +++ b/code/using_GO/pla/T15_7_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_7_3001_4000.R b/code/using_GO/pla/T15_7_3001_4000.R index 49a5a815c10a2d6fd84303e303106c4d40d68de1..c7186ef8bbf6f388340c2bda1307ef573e26b076 100644 --- a/code/using_GO/pla/T15_7_3001_4000.R +++ b/code/using_GO/pla/T15_7_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_7_4001_5000.R b/code/using_GO/pla/T15_7_4001_5000.R index 824c87897829137f7c2221aca2dbf5e915141a29..5696c58b84b941e3241f7e3813534e7fe48bcbd7 100644 --- a/code/using_GO/pla/T15_7_4001_5000.R +++ b/code/using_GO/pla/T15_7_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_7_5001_6000.R b/code/using_GO/pla/T15_7_5001_6000.R index 92c45f8e0c2cd6c759b80bc179d845dcf53e1a13..fbb5564b4c738fb773abf482718218e7de6d17b1 100644 --- a/code/using_GO/pla/T15_7_5001_6000.R +++ b/code/using_GO/pla/T15_7_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_7_6001_7297.R b/code/using_GO/pla/T15_7_6001_7297.R index 58ee2a30618b88e1f44aba51e1ce0347e8229dae..70658efda8cf10e83f45e6e003253d1b0aed4721 100644 --- a/code/using_GO/pla/T15_7_6001_7297.R +++ b/code/using_GO/pla/T15_7_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_8_1001_2000.R b/code/using_GO/pla/T15_8_1001_2000.R index a903e504739161b8a10284ea2870e9489dbabc1b..194300521deab72df7357d8d8179a856aab439d9 100644 --- a/code/using_GO/pla/T15_8_1001_2000.R +++ b/code/using_GO/pla/T15_8_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_8_1_1000.R b/code/using_GO/pla/T15_8_1_1000.R index 29b7426b0a68ec9d31bbc0b4518907a6833dfbb0..e8bd77b6d2f1b481e8d279b2fb8805e51e0d4553 100644 --- a/code/using_GO/pla/T15_8_1_1000.R +++ b/code/using_GO/pla/T15_8_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_8_2001_3000.R b/code/using_GO/pla/T15_8_2001_3000.R index 8e9ff544a3a1c8babec026ea0693e4b4ee28d26a..3b7e2153e40af4f3383f410e55b7cde44f8cb2e9 100644 --- a/code/using_GO/pla/T15_8_2001_3000.R +++ b/code/using_GO/pla/T15_8_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_8_3001_4000.R b/code/using_GO/pla/T15_8_3001_4000.R index 098466ead9c5735af647730c40d5d1a5b6dea627..1a9215b6bf131c2c837630eccc908b4b7b9ae98e 100644 --- a/code/using_GO/pla/T15_8_3001_4000.R +++ b/code/using_GO/pla/T15_8_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_8_4001_5000.R b/code/using_GO/pla/T15_8_4001_5000.R index 8c0f44c474ec1c026b35e94875e4b79e44feb1d6..1123714ee043e323fb89f91473a0502eda71cebc 100644 --- a/code/using_GO/pla/T15_8_4001_5000.R +++ b/code/using_GO/pla/T15_8_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_8_5001_6000.R b/code/using_GO/pla/T15_8_5001_6000.R index 6b7141f554583a51710e692ab3028e77ad221036..eb806fa5a18f5832cf6870010425066a46c2e96d 100644 --- a/code/using_GO/pla/T15_8_5001_6000.R +++ b/code/using_GO/pla/T15_8_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T15_8_6001_7297.R b/code/using_GO/pla/T15_8_6001_7297.R index 94a92dfbfefef7d1b8071c00aa4a26ead26c6f4c..e7ae6b446dd5dc37cd9d5e0c2ab51f52612652c9 100644 --- a/code/using_GO/pla/T15_8_6001_7297.R +++ b/code/using_GO/pla/T15_8_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T15_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_1_1001_2000.R b/code/using_GO/pla/T16_1_1001_2000.R index 15c58c9d2647d1d12188a3f4fa2f61be5101c3e4..87f433d67c60c4a9b801bdfc0f85e778feeaf874 100644 --- a/code/using_GO/pla/T16_1_1001_2000.R +++ b/code/using_GO/pla/T16_1_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_1_1_1000.R b/code/using_GO/pla/T16_1_1_1000.R index 5859c7dd44dfe82d0d194d0eb24c84049fb606aa..ef8a83aa8b699df3807f1eae64d179e5ca89a581 100644 --- a/code/using_GO/pla/T16_1_1_1000.R +++ b/code/using_GO/pla/T16_1_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_1_2001_3000.R b/code/using_GO/pla/T16_1_2001_3000.R index b98a17a41e5efa940660a37f6fe9d44c7156cf38..5eee3a837cfac3beb59a6eeede7c67cfe1ed69cb 100644 --- a/code/using_GO/pla/T16_1_2001_3000.R +++ b/code/using_GO/pla/T16_1_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_1_3001_4000.R b/code/using_GO/pla/T16_1_3001_4000.R index d50b02638501e82c055182be14a573d95122f588..543b4403b1e1d33946c3e9020af5eeef04129fd6 100644 --- a/code/using_GO/pla/T16_1_3001_4000.R +++ b/code/using_GO/pla/T16_1_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_1_4001_5000.R b/code/using_GO/pla/T16_1_4001_5000.R index 9b96548df2dede9329fa57e4eaac8cd770bd83cb..383b304d6bd93f43837c008fba1c8ce4533216b7 100644 --- a/code/using_GO/pla/T16_1_4001_5000.R +++ b/code/using_GO/pla/T16_1_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_1_5001_6000.R b/code/using_GO/pla/T16_1_5001_6000.R index 8e3db7d393686c871b8be08639e5b47dd21dc532..298fee2c83675647beb0ec3575808b7f156ea624 100644 --- a/code/using_GO/pla/T16_1_5001_6000.R +++ b/code/using_GO/pla/T16_1_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_1_6001_7297.R b/code/using_GO/pla/T16_1_6001_7297.R index 136d48f7f1772b84f96a9ef5e6036cf418958463..f0bfa496ab0ecc2968ade145e23099a740de2915 100644 --- a/code/using_GO/pla/T16_1_6001_7297.R +++ b/code/using_GO/pla/T16_1_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_2_1001_2000.R b/code/using_GO/pla/T16_2_1001_2000.R index e7d6af6ed30293ae5218769d28f8a121886c9eab..bdcef89eb7047ef7e8a14466b50e477eb77783a2 100644 --- a/code/using_GO/pla/T16_2_1001_2000.R +++ b/code/using_GO/pla/T16_2_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_2_1_1000.R b/code/using_GO/pla/T16_2_1_1000.R index b18897dd3c604a5570ab5f2d817fea5541df31c6..e1c836caa5a65b02e20ab1b8603c7b26f7410c5d 100644 --- a/code/using_GO/pla/T16_2_1_1000.R +++ b/code/using_GO/pla/T16_2_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_2_2001_3000.R b/code/using_GO/pla/T16_2_2001_3000.R index 69c45b4d1236bc050a0c1587e25d45f7f5f201d2..9198413060cf8ed12f6fb52291839eeecc0583a4 100644 --- a/code/using_GO/pla/T16_2_2001_3000.R +++ b/code/using_GO/pla/T16_2_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_2_3001_4000.R b/code/using_GO/pla/T16_2_3001_4000.R index 8c470465b772996b8ef9abbd91213d445870fc04..e0a20930a97f5ede05960a63b7d3da6b55ff5221 100644 --- a/code/using_GO/pla/T16_2_3001_4000.R +++ b/code/using_GO/pla/T16_2_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_2_4001_5000.R b/code/using_GO/pla/T16_2_4001_5000.R index 78ed0a37db7b0d16823920794eb766c3f2dd5a6d..963d5534b236e4b3e92487207ec729d7b987eedd 100644 --- a/code/using_GO/pla/T16_2_4001_5000.R +++ b/code/using_GO/pla/T16_2_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_2_5001_6000.R b/code/using_GO/pla/T16_2_5001_6000.R index ffb62ea13b2e604aff20a7aa297a53dbbfc2a301..51b9d06cc93f2b1d919cda2ef3bf7275bd097174 100644 --- a/code/using_GO/pla/T16_2_5001_6000.R +++ b/code/using_GO/pla/T16_2_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_2_6001_7297.R b/code/using_GO/pla/T16_2_6001_7297.R index 20f381b1954755ab7866cf88914949175acb0ec3..e5dca94a45cf2417200654e277a2c80913682860 100644 --- a/code/using_GO/pla/T16_2_6001_7297.R +++ b/code/using_GO/pla/T16_2_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_3_1001_2000.R b/code/using_GO/pla/T16_3_1001_2000.R index 0c2b84f57fa0ad27f05af53c95aece3cee97fe1f..e1c22862876159eae897e31af07d2f4ae8f29f59 100644 --- a/code/using_GO/pla/T16_3_1001_2000.R +++ b/code/using_GO/pla/T16_3_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_3_1_1000.R b/code/using_GO/pla/T16_3_1_1000.R index 3eef118f4ace058f0ac4acb436120a680ec570e2..c093d4ce2017cf80da3a5dba3612470919146df7 100644 --- a/code/using_GO/pla/T16_3_1_1000.R +++ b/code/using_GO/pla/T16_3_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_3_2001_3000.R b/code/using_GO/pla/T16_3_2001_3000.R index d84db561acfe4ae65340758f3b3fde85b2ff7c00..6bb1d82cb6e273d1d6832d856e6d9c483c3206e3 100644 --- a/code/using_GO/pla/T16_3_2001_3000.R +++ b/code/using_GO/pla/T16_3_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_3_3001_4000.R b/code/using_GO/pla/T16_3_3001_4000.R index 6164a25cca47cf3ebc7cc9fb0fdc893c22c47e36..0b6349b4b44df187657bc08f51852c458a17d57d 100644 --- a/code/using_GO/pla/T16_3_3001_4000.R +++ b/code/using_GO/pla/T16_3_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_3_4001_5000.R b/code/using_GO/pla/T16_3_4001_5000.R index 95234f4916fd78c9c8ebc9232e4e7c30091343d9..edf0b8ff69592275718ad4619520d8eaf4af62b1 100644 --- a/code/using_GO/pla/T16_3_4001_5000.R +++ b/code/using_GO/pla/T16_3_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_3_5001_6000.R b/code/using_GO/pla/T16_3_5001_6000.R index 13231fcd8e03c2e0376ab9d94eba213766943155..5722cb4047a2afd4ddfb53cc4763536e60f0060d 100644 --- a/code/using_GO/pla/T16_3_5001_6000.R +++ b/code/using_GO/pla/T16_3_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_3_6001_7297.R b/code/using_GO/pla/T16_3_6001_7297.R index 9df06b48e4ea4ee271211d93d5143ca274ef0204..b19bd5ea3c0d90c07a143cf2dea5113049490e28 100644 --- a/code/using_GO/pla/T16_3_6001_7297.R +++ b/code/using_GO/pla/T16_3_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_4_1001_2000.R b/code/using_GO/pla/T16_4_1001_2000.R index e0d44efe163619c9040c0bc9a1f8e250798538b4..45c55fb079a83fd4b970cd8151c535be4dc77289 100644 --- a/code/using_GO/pla/T16_4_1001_2000.R +++ b/code/using_GO/pla/T16_4_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_4_1_1000.R b/code/using_GO/pla/T16_4_1_1000.R index 5cd0a6a0c0dbeb55b0d1aec3c37cd2f7b5ca2ce1..88c17b0a5a66aa5928423722b7fbc907eff72a7d 100644 --- a/code/using_GO/pla/T16_4_1_1000.R +++ b/code/using_GO/pla/T16_4_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_4_2001_3000.R b/code/using_GO/pla/T16_4_2001_3000.R index 0f6358c70c4eb6a25ed87df2da3942e88f4bbcd8..177dff699b48c5038e38c3facb64324b104d2a21 100644 --- a/code/using_GO/pla/T16_4_2001_3000.R +++ b/code/using_GO/pla/T16_4_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_4_3001_4000.R b/code/using_GO/pla/T16_4_3001_4000.R index ed80345abf6e34ef09f036615d3bb7876914928e..b38d7c7e5361d55ce56d8d91af73b022e6659753 100644 --- a/code/using_GO/pla/T16_4_3001_4000.R +++ b/code/using_GO/pla/T16_4_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_4_4001_5000.R b/code/using_GO/pla/T16_4_4001_5000.R index af195531616501059639b34ab441a51c22ca3fff..a911201c274829303955945e98f8cda9128ae193 100644 --- a/code/using_GO/pla/T16_4_4001_5000.R +++ b/code/using_GO/pla/T16_4_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_4_5001_6000.R b/code/using_GO/pla/T16_4_5001_6000.R index 6f9695befb00e3615817e7fe553190c34ca82ba0..ccde4801e286fe3ba6e25ee592ce65ea2d806ce0 100644 --- a/code/using_GO/pla/T16_4_5001_6000.R +++ b/code/using_GO/pla/T16_4_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_4_6001_7297.R b/code/using_GO/pla/T16_4_6001_7297.R index 83f9c5e3cca93d1ef3b69c6fc778904fb659116f..f4288b0bca9086356a17e9ee829b2285b5ab8a6b 100644 --- a/code/using_GO/pla/T16_4_6001_7297.R +++ b/code/using_GO/pla/T16_4_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_5_1001_2000.R b/code/using_GO/pla/T16_5_1001_2000.R index ff653c6ff1d4409961b8cf66b2c280bf67640012..291bcaa59597b3b94ab73aaaa3fff6cfe182b754 100644 --- a/code/using_GO/pla/T16_5_1001_2000.R +++ b/code/using_GO/pla/T16_5_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_5_1_1000.R b/code/using_GO/pla/T16_5_1_1000.R index 4d3c582f5cb6faa884c614cca064b3e0a74b34a2..e8e19224094b2e43ce8c151d700564dae243640c 100644 --- a/code/using_GO/pla/T16_5_1_1000.R +++ b/code/using_GO/pla/T16_5_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_5_2001_3000.R b/code/using_GO/pla/T16_5_2001_3000.R index 7c24bf9a9e6bc7a1b0dae22e47ea74a9e8ffc7e1..370666ffa911e76e98f5f016e43eef586a087e52 100644 --- a/code/using_GO/pla/T16_5_2001_3000.R +++ b/code/using_GO/pla/T16_5_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_5_3001_4000.R b/code/using_GO/pla/T16_5_3001_4000.R index ca125a1bb01bdd64bf60dca1466a54eed15ca56c..29434efc392b5543127c50b59603fe899ed808f0 100644 --- a/code/using_GO/pla/T16_5_3001_4000.R +++ b/code/using_GO/pla/T16_5_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_5_4001_5000.R b/code/using_GO/pla/T16_5_4001_5000.R index 51fb1d55ae64187f984d1ccb6a25e02e0e97ff9a..f1058c62d484356a63ed21f1d8b892e1efd003ba 100644 --- a/code/using_GO/pla/T16_5_4001_5000.R +++ b/code/using_GO/pla/T16_5_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_5_5001_6000.R b/code/using_GO/pla/T16_5_5001_6000.R index 8c07cb013bc18e6e1b55ecfc1fc85369eca68ee7..26423fdd5394ff5de9215106cae29f33d375467b 100644 --- a/code/using_GO/pla/T16_5_5001_6000.R +++ b/code/using_GO/pla/T16_5_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_5_6001_7297.R b/code/using_GO/pla/T16_5_6001_7297.R index 5f8f3a12f2c305f083a4d85ab0b75e85de4febfa..0c460ffd752532a325c5854780560edb77e72977 100644 --- a/code/using_GO/pla/T16_5_6001_7297.R +++ b/code/using_GO/pla/T16_5_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_6_1001_2000.R b/code/using_GO/pla/T16_6_1001_2000.R index fb207ad446619c0e4547fc3a4c2de1e8069047ed..5a4c3cb19563360eaae7d6f6b14208dad4601d32 100644 --- a/code/using_GO/pla/T16_6_1001_2000.R +++ b/code/using_GO/pla/T16_6_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_6_1_1000.R b/code/using_GO/pla/T16_6_1_1000.R index dcabdb75a5d8af5a22a71cfec3e52771504eeda2..eea5b2a4f850b2a4b3f6e5523bd787800495715e 100644 --- a/code/using_GO/pla/T16_6_1_1000.R +++ b/code/using_GO/pla/T16_6_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_6_2001_3000.R b/code/using_GO/pla/T16_6_2001_3000.R index 8fc0e62ba7895daf322c325203196eccf2572da7..f56010dd3ed4364ac137ed96647224923f601b2b 100644 --- a/code/using_GO/pla/T16_6_2001_3000.R +++ b/code/using_GO/pla/T16_6_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_6_3001_4000.R b/code/using_GO/pla/T16_6_3001_4000.R index 38e7f577dc79d6ddac436a3b88c60ce5907cf1d9..335c918eba79991c706a7baa3860249493037f8a 100644 --- a/code/using_GO/pla/T16_6_3001_4000.R +++ b/code/using_GO/pla/T16_6_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_6_4001_5000.R b/code/using_GO/pla/T16_6_4001_5000.R index 7dd77a07df88fe777687c4d083bec2c7cb239c88..879695e8641760b748f3ca6492d66b25a676d6bd 100644 --- a/code/using_GO/pla/T16_6_4001_5000.R +++ b/code/using_GO/pla/T16_6_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_6_5001_6000.R b/code/using_GO/pla/T16_6_5001_6000.R index 0d1b710b021d949f6020519c206dce6ecc33656a..c460fdf14a3ed2db433afc47a5f911ace6d0c63e 100644 --- a/code/using_GO/pla/T16_6_5001_6000.R +++ b/code/using_GO/pla/T16_6_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_6_6001_7297.R b/code/using_GO/pla/T16_6_6001_7297.R index 803624b3978025cd738c4aa4a7b2033b15eb8074..24765341c362a35bfdbfec8c17f4f189d03113b9 100644 --- a/code/using_GO/pla/T16_6_6001_7297.R +++ b/code/using_GO/pla/T16_6_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_7_1001_2000.R b/code/using_GO/pla/T16_7_1001_2000.R index a39cc0cce8145c6c7242e32520a3b00ffcfb104f..9da9b138a8ffca608453e0627e3784c7f74d422d 100644 --- a/code/using_GO/pla/T16_7_1001_2000.R +++ b/code/using_GO/pla/T16_7_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_7_1_1000.R b/code/using_GO/pla/T16_7_1_1000.R index a39d072c948a11a669d097267081c4003f51d864..d4b8ccf8e59f87c9a368d0989bbd62ba952221d7 100644 --- a/code/using_GO/pla/T16_7_1_1000.R +++ b/code/using_GO/pla/T16_7_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_7_2001_3000.R b/code/using_GO/pla/T16_7_2001_3000.R index bab3ffc71816f5b8caeb14d6b180b3ed9d9c9895..4de6071b0dd14007a06500d6348319d45bf20f67 100644 --- a/code/using_GO/pla/T16_7_2001_3000.R +++ b/code/using_GO/pla/T16_7_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_7_3001_4000.R b/code/using_GO/pla/T16_7_3001_4000.R index 57956bd8db6de36f24c3df2c0fbe69bcbde4e231..b10199f90e189f7aba135d1798c8a5f8c4be9d18 100644 --- a/code/using_GO/pla/T16_7_3001_4000.R +++ b/code/using_GO/pla/T16_7_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_7_4001_5000.R b/code/using_GO/pla/T16_7_4001_5000.R index 43161859ac830b7448dd1cb55ed17eafe3bd4ad3..70013047790e970ad0b1b8cb54ec9b1edbb8242b 100644 --- a/code/using_GO/pla/T16_7_4001_5000.R +++ b/code/using_GO/pla/T16_7_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_7_5001_6000.R b/code/using_GO/pla/T16_7_5001_6000.R index 97b443982bd9856e1c330339ac767e44457fa6f8..3ac02edf6db814e9d35a08e7299c7899eee251ea 100644 --- a/code/using_GO/pla/T16_7_5001_6000.R +++ b/code/using_GO/pla/T16_7_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_7_6001_7297.R b/code/using_GO/pla/T16_7_6001_7297.R index db9166b4f85f59845adf994a26ada0201a5bb93a..9f97f20783e3ba23e11830e1114c3eb60574c617 100644 --- a/code/using_GO/pla/T16_7_6001_7297.R +++ b/code/using_GO/pla/T16_7_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_8_1001_2000.R b/code/using_GO/pla/T16_8_1001_2000.R index 79d4a6a3628bd3e5a81ca67aaddefd84e31ed506..8a4db1392c44aceb1e30b8fdbcc82afee80bf1ed 100644 --- a/code/using_GO/pla/T16_8_1001_2000.R +++ b/code/using_GO/pla/T16_8_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_8_1_1000.R b/code/using_GO/pla/T16_8_1_1000.R index 781b0fa0812c753efdc9412d8d2b4243186035b4..b7b41540e134f58f720ce6a4809dcf223ec0c23a 100644 --- a/code/using_GO/pla/T16_8_1_1000.R +++ b/code/using_GO/pla/T16_8_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_8_2001_3000.R b/code/using_GO/pla/T16_8_2001_3000.R index f1a1c6cac18f9d6c6fa2b55c8c76883c66c182a1..158fff15bd91723fd6031fb33e44bd8e89dbb0e5 100644 --- a/code/using_GO/pla/T16_8_2001_3000.R +++ b/code/using_GO/pla/T16_8_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_8_3001_4000.R b/code/using_GO/pla/T16_8_3001_4000.R index 1969932474e34a59a196fda10d2685e7a36b544a..e7a9ed4ca02758fd7c07dab70297f26a2071d300 100644 --- a/code/using_GO/pla/T16_8_3001_4000.R +++ b/code/using_GO/pla/T16_8_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_8_4001_5000.R b/code/using_GO/pla/T16_8_4001_5000.R index 13cd2b5d7e61203b9acfbc82c1dc0edd514d5191..ca097de623a6d118f87bfa7db82b3b3ac4257404 100644 --- a/code/using_GO/pla/T16_8_4001_5000.R +++ b/code/using_GO/pla/T16_8_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_8_5001_6000.R b/code/using_GO/pla/T16_8_5001_6000.R index 02ed2cb1f197ca929dec41fc19deb91e86d0957a..64ec4da3739fdec344efb6a3246be118e5792c0e 100644 --- a/code/using_GO/pla/T16_8_5001_6000.R +++ b/code/using_GO/pla/T16_8_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T16_8_6001_7297.R b/code/using_GO/pla/T16_8_6001_7297.R index af6422c90d47c62142c2fd84b323424b20f8d410..de0261003177c8eff4ecf51753d290a326fac4d9 100644 --- a/code/using_GO/pla/T16_8_6001_7297.R +++ b/code/using_GO/pla/T16_8_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T16_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_1_1001_2000.R b/code/using_GO/pla/T17_1_1001_2000.R index 4d1f06a11b28dd869327e496793eaa50f0d7c328..96285d78e56d63da5af66eb982e4245fc97e69a0 100644 --- a/code/using_GO/pla/T17_1_1001_2000.R +++ b/code/using_GO/pla/T17_1_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_1_1_1000.R b/code/using_GO/pla/T17_1_1_1000.R index f1828d52f0f3a72b095ee1b349129365fd10f949..766237a9599d2b34019799c73adf8453bf54f8ad 100644 --- a/code/using_GO/pla/T17_1_1_1000.R +++ b/code/using_GO/pla/T17_1_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_1_2001_3000.R b/code/using_GO/pla/T17_1_2001_3000.R index 3fa741e7e584028cef23ced0c1f288df4189d52f..45fe9120ce0362954ed1e6bf11c31f450b38ccb0 100644 --- a/code/using_GO/pla/T17_1_2001_3000.R +++ b/code/using_GO/pla/T17_1_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_1_3001_4000.R b/code/using_GO/pla/T17_1_3001_4000.R index c780745bf674c043b321d0e7512019b4862e31f1..9aaa5711fa0ae552a676cf79c7dd5c66c9d76478 100644 --- a/code/using_GO/pla/T17_1_3001_4000.R +++ b/code/using_GO/pla/T17_1_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_1_4001_5000.R b/code/using_GO/pla/T17_1_4001_5000.R index b21d59183cd203b06541ff8d4caaa5803ed81da2..052c1040ffc20e95040bce9ee3d29dde3be8f868 100644 --- a/code/using_GO/pla/T17_1_4001_5000.R +++ b/code/using_GO/pla/T17_1_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_1_5001_6000.R b/code/using_GO/pla/T17_1_5001_6000.R index d3b15f22a6bdb336db32732eb2734847532ccffb..667241431d15a838f974559dfce49eba2b1a3099 100644 --- a/code/using_GO/pla/T17_1_5001_6000.R +++ b/code/using_GO/pla/T17_1_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_1_6001_7297.R b/code/using_GO/pla/T17_1_6001_7297.R index d99c2155dd83a56994305485405223ace5a2363d..ecfd9bd2160ff61f3934d787ca3af73b0b307735 100644 --- a/code/using_GO/pla/T17_1_6001_7297.R +++ b/code/using_GO/pla/T17_1_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_2_1001_2000.R b/code/using_GO/pla/T17_2_1001_2000.R index c9ab35722f314847504755dd666f7c7ccbc7706b..20f7f485fcc300a2dbe3b3343474cdae2fec46fa 100644 --- a/code/using_GO/pla/T17_2_1001_2000.R +++ b/code/using_GO/pla/T17_2_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_2_1_1000.R b/code/using_GO/pla/T17_2_1_1000.R index 21c36380f0332689760fe944626ffcb2d4312bbe..b96ef0e16f58a4ad7a8dfeba9a3535c5e0d81c27 100644 --- a/code/using_GO/pla/T17_2_1_1000.R +++ b/code/using_GO/pla/T17_2_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_2_2001_3000.R b/code/using_GO/pla/T17_2_2001_3000.R index 1b5235f52b25b58ec354752827b95ed51a7bf523..5c5005310e29429b3670f2a214635a2e7eda2157 100644 --- a/code/using_GO/pla/T17_2_2001_3000.R +++ b/code/using_GO/pla/T17_2_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_2_3001_4000.R b/code/using_GO/pla/T17_2_3001_4000.R index 9bb76504b3bb31d357ff3633a8ac0b02539544ab..471cb6f207ae243b010b46c1e8f1d2cdff0fa839 100644 --- a/code/using_GO/pla/T17_2_3001_4000.R +++ b/code/using_GO/pla/T17_2_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_2_4001_5000.R b/code/using_GO/pla/T17_2_4001_5000.R index 9bc8e48631232e35387e412ed0c91d8e696023bc..2ab04011bbdcb9f70360f063b0208a029de9c6b0 100644 --- a/code/using_GO/pla/T17_2_4001_5000.R +++ b/code/using_GO/pla/T17_2_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_2_5001_6000.R b/code/using_GO/pla/T17_2_5001_6000.R index d83851d8417a2882c7eb1aa73042e7985447ede6..a8da5fae4b55b8fec34024aa190796550095b630 100644 --- a/code/using_GO/pla/T17_2_5001_6000.R +++ b/code/using_GO/pla/T17_2_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_2_6001_7297.R b/code/using_GO/pla/T17_2_6001_7297.R index d39f74a49427c2f8e338147e192afc47e498bb84..be45dd391a59b9ea3d80ccf7ce998ec57b8b06cc 100644 --- a/code/using_GO/pla/T17_2_6001_7297.R +++ b/code/using_GO/pla/T17_2_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_3_1001_2000.R b/code/using_GO/pla/T17_3_1001_2000.R index 92fb34675e67cc9a5b62373fc758c701fe3c8793..e91dea610a28852e06d1c99a3b60d84e18ec8289 100644 --- a/code/using_GO/pla/T17_3_1001_2000.R +++ b/code/using_GO/pla/T17_3_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_3_1_1000.R b/code/using_GO/pla/T17_3_1_1000.R index dd3f119b3e52d27367a50fe2c38372390c736da5..4d67879433fe577b29224116ff8baffb26cfb6e8 100644 --- a/code/using_GO/pla/T17_3_1_1000.R +++ b/code/using_GO/pla/T17_3_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_3_2001_3000.R b/code/using_GO/pla/T17_3_2001_3000.R index 5896ef58a6c0dfb3333b37ad971a215f23f1d499..74154a0a37fd073ee3e819a3fa8329aea54d1017 100644 --- a/code/using_GO/pla/T17_3_2001_3000.R +++ b/code/using_GO/pla/T17_3_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_3_3001_4000.R b/code/using_GO/pla/T17_3_3001_4000.R index d0e95d104bb676bfa3bedb228d76f739c5ca5acf..2e6035a33ccacd363e1a68fca64da5a53f4c5472 100644 --- a/code/using_GO/pla/T17_3_3001_4000.R +++ b/code/using_GO/pla/T17_3_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_3_4001_5000.R b/code/using_GO/pla/T17_3_4001_5000.R index bf5c72de5975c76070712bf91bddddaea5466bb8..6a74a7bd31bb84ba3739090e1780ec0aca70e51b 100644 --- a/code/using_GO/pla/T17_3_4001_5000.R +++ b/code/using_GO/pla/T17_3_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_3_5001_6000.R b/code/using_GO/pla/T17_3_5001_6000.R index 5a8711545983e17d852f6f1732ac7f49a9aae826..2ff4120b74114421b6ec3733ccdaa4e6fec613d3 100644 --- a/code/using_GO/pla/T17_3_5001_6000.R +++ b/code/using_GO/pla/T17_3_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_3_6001_7297.R b/code/using_GO/pla/T17_3_6001_7297.R index e8732e5cc484d81a9c2eb36673de9bacbf4157ff..6ba5d85c3302c5826584764f939e79e817b87d04 100644 --- a/code/using_GO/pla/T17_3_6001_7297.R +++ b/code/using_GO/pla/T17_3_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_4_1001_2000.R b/code/using_GO/pla/T17_4_1001_2000.R index 19cd99b84d0c002f585e5e3eef0dbab14c8ce3ed..9f0778f8d2e4df8b1292ed84884fba7235d0f174 100644 --- a/code/using_GO/pla/T17_4_1001_2000.R +++ b/code/using_GO/pla/T17_4_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_4_1_1000.R b/code/using_GO/pla/T17_4_1_1000.R index cc879269c04903d47b6cd88cf9d3b48a11329d40..bc5c859270d12080d51c1fd16cf97bf59a42a7fc 100644 --- a/code/using_GO/pla/T17_4_1_1000.R +++ b/code/using_GO/pla/T17_4_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_4_2001_3000.R b/code/using_GO/pla/T17_4_2001_3000.R index 5eb4e629649f655a262e0ceeebdbc74d2e484676..4624372be0d64e6bf64994c483f88433b486e7f4 100644 --- a/code/using_GO/pla/T17_4_2001_3000.R +++ b/code/using_GO/pla/T17_4_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_4_3001_4000.R b/code/using_GO/pla/T17_4_3001_4000.R index edf1dfb5a3e1441a682408595a8d1067eafe291c..861ef2c42d10f7ca01791b28fa04c16a8a2de2ea 100644 --- a/code/using_GO/pla/T17_4_3001_4000.R +++ b/code/using_GO/pla/T17_4_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_4_4001_5000.R b/code/using_GO/pla/T17_4_4001_5000.R index 9f1b98f6380306ac85416ee3f119da2a76e2194e..c9b79c0197c9c2c399d6e3c6c7a86b28a5469b23 100644 --- a/code/using_GO/pla/T17_4_4001_5000.R +++ b/code/using_GO/pla/T17_4_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_4_5001_6000.R b/code/using_GO/pla/T17_4_5001_6000.R index d3f9d0a48b39811bab411a7f1f2edf97018121fb..549b5d6021a11f1bc426e2a18d36adebc7974263 100644 --- a/code/using_GO/pla/T17_4_5001_6000.R +++ b/code/using_GO/pla/T17_4_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_4_6001_7297.R b/code/using_GO/pla/T17_4_6001_7297.R index b773a9cc67a81a76f21316b775db75dc3f470fcd..dc72a19e4094b78841dc9425cab0010747bc1413 100644 --- a/code/using_GO/pla/T17_4_6001_7297.R +++ b/code/using_GO/pla/T17_4_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_5_1001_2000.R b/code/using_GO/pla/T17_5_1001_2000.R index 6adad7610e8bf57a60a2576627ce06b530dcd96b..51ec6e8ccaee676cb8406269319fcbf6bf509567 100644 --- a/code/using_GO/pla/T17_5_1001_2000.R +++ b/code/using_GO/pla/T17_5_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_5_1_1000.R b/code/using_GO/pla/T17_5_1_1000.R index d423904cac8a53dcfaa8738834d8f3f5425c309f..3948b76c67f584b565f8bc7a5bdb0f6319b972e9 100644 --- a/code/using_GO/pla/T17_5_1_1000.R +++ b/code/using_GO/pla/T17_5_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_5_2001_3000.R b/code/using_GO/pla/T17_5_2001_3000.R index 365c4cad47c0eb509e1b1246833ccbff669cff55..84cd25929a50d01d65c35b5e635cec72347ec282 100644 --- a/code/using_GO/pla/T17_5_2001_3000.R +++ b/code/using_GO/pla/T17_5_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_5_3001_4000.R b/code/using_GO/pla/T17_5_3001_4000.R index 5a70ee43fd51f9c007d0710cc1bd3741c4e1c5fc..8368d795910d358fc2af144be425595a8769c190 100644 --- a/code/using_GO/pla/T17_5_3001_4000.R +++ b/code/using_GO/pla/T17_5_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_5_4001_5000.R b/code/using_GO/pla/T17_5_4001_5000.R index fbd74007c60faeac17a82ceb910bbe8906df8185..2831d3b9c1230c3f7354a5d6ba9ca52e97657d1e 100644 --- a/code/using_GO/pla/T17_5_4001_5000.R +++ b/code/using_GO/pla/T17_5_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_5_5001_6000.R b/code/using_GO/pla/T17_5_5001_6000.R index f6d90f2a225d50003366199e8b88ca2d3645c620..32d59de3fbe7320ff55137594ee2c7b9ec2acc57 100644 --- a/code/using_GO/pla/T17_5_5001_6000.R +++ b/code/using_GO/pla/T17_5_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_5_6001_7297.R b/code/using_GO/pla/T17_5_6001_7297.R index 94e5775594620fe45eca955c94a2a30464a4b9ca..2158e86b41ee1348008268fc0d4bfaaec0897a31 100644 --- a/code/using_GO/pla/T17_5_6001_7297.R +++ b/code/using_GO/pla/T17_5_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_6_1001_2000.R b/code/using_GO/pla/T17_6_1001_2000.R index 6c041cdb79a3c1a9d364924f176d89bb5797e933..56e99b6d263c18883b16fbb5c0cf5cd745008ffa 100644 --- a/code/using_GO/pla/T17_6_1001_2000.R +++ b/code/using_GO/pla/T17_6_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_6_1_1000.R b/code/using_GO/pla/T17_6_1_1000.R index 46860aea7ef3249e35b9676b64445c5c5d61395d..004148ef041b9819d17c94a4d78aa916552e4058 100644 --- a/code/using_GO/pla/T17_6_1_1000.R +++ b/code/using_GO/pla/T17_6_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_6_2001_3000.R b/code/using_GO/pla/T17_6_2001_3000.R index 41e9f52b307f4d8e9bc9012f83aa10092cb1517a..09fc419fef48532d4e3aefd803b6086dc2892cc6 100644 --- a/code/using_GO/pla/T17_6_2001_3000.R +++ b/code/using_GO/pla/T17_6_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_6_3001_4000.R b/code/using_GO/pla/T17_6_3001_4000.R index 165d60b26cd46fc31d625c9837966aa47f5064c6..295532ff04148776d79ee34ed146fc2adf9be37a 100644 --- a/code/using_GO/pla/T17_6_3001_4000.R +++ b/code/using_GO/pla/T17_6_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_6_4001_5000.R b/code/using_GO/pla/T17_6_4001_5000.R index abe1608c6fe4df3a6174227505d22fd9e4a73908..15a3fe18d7b0b793ccf68619ab7382ec3c27adf9 100644 --- a/code/using_GO/pla/T17_6_4001_5000.R +++ b/code/using_GO/pla/T17_6_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_6_5001_6000.R b/code/using_GO/pla/T17_6_5001_6000.R index 96c153099880fc37bb33b93ec736255f9f88ec8e..84cedac2435a9699cee9c00a1f255c4f463aba12 100644 --- a/code/using_GO/pla/T17_6_5001_6000.R +++ b/code/using_GO/pla/T17_6_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_6_6001_7297.R b/code/using_GO/pla/T17_6_6001_7297.R index f21d37ba37977222da28f4dca4b171ff98b7befa..2d5c201d37506b80712ef2b865eef34e8563622e 100644 --- a/code/using_GO/pla/T17_6_6001_7297.R +++ b/code/using_GO/pla/T17_6_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_7_1001_2000.R b/code/using_GO/pla/T17_7_1001_2000.R index 04828866e107622a15058ae58189ffcd9b9c9d2a..376a81fde12eb7f9b2798a47c5e5305a08fd94f9 100644 --- a/code/using_GO/pla/T17_7_1001_2000.R +++ b/code/using_GO/pla/T17_7_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_7_1_1000.R b/code/using_GO/pla/T17_7_1_1000.R index bfcf41e7d4850edee24e99251b98005f49f73896..a4ace90c36ec8efb85458f8338f88d7cdeb729f1 100644 --- a/code/using_GO/pla/T17_7_1_1000.R +++ b/code/using_GO/pla/T17_7_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_7_2001_3000.R b/code/using_GO/pla/T17_7_2001_3000.R index 732e7ffe947d64dbc47ad42cf177bff165e3667b..3290f139551c26c9dffe3b1a7801a02a5230c216 100644 --- a/code/using_GO/pla/T17_7_2001_3000.R +++ b/code/using_GO/pla/T17_7_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_7_3001_4000.R b/code/using_GO/pla/T17_7_3001_4000.R index 990353283d71679dacc28e8d4c0b91df086fafb8..0aaf4d1360fe4de79437989f672d60ddbdc5a380 100644 --- a/code/using_GO/pla/T17_7_3001_4000.R +++ b/code/using_GO/pla/T17_7_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_7_4001_5000.R b/code/using_GO/pla/T17_7_4001_5000.R index cf0bd608c555461f8f4894e593fc38e84ce8c15a..4619e5f545c297e6de5851f0973639a8afcfb45d 100644 --- a/code/using_GO/pla/T17_7_4001_5000.R +++ b/code/using_GO/pla/T17_7_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_7_5001_6000.R b/code/using_GO/pla/T17_7_5001_6000.R index 7ea304914239a39649a6a24bfe2c860f33a046c3..39e4cb6ede88b7f0b527ccd90a1aa2a89a378604 100644 --- a/code/using_GO/pla/T17_7_5001_6000.R +++ b/code/using_GO/pla/T17_7_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_7_6001_7297.R b/code/using_GO/pla/T17_7_6001_7297.R index aeda6a2868247b58877f3c6721fd7fefd771a732..b4ce0fefbad4444682508b7f806021cc9e17fdd1 100644 --- a/code/using_GO/pla/T17_7_6001_7297.R +++ b/code/using_GO/pla/T17_7_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_8_1001_2000.R b/code/using_GO/pla/T17_8_1001_2000.R index 4484afb9d2c713b861db08e6c9afd89da8cfb03a..8d49cce3541c927492bea2c9dfc5596544ff9955 100644 --- a/code/using_GO/pla/T17_8_1001_2000.R +++ b/code/using_GO/pla/T17_8_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_8_1_1000.R b/code/using_GO/pla/T17_8_1_1000.R index 17ff57712fdfa37eb60034b70d01e4a4ba4a74f4..c53042957125c9435020dd9728f7e212b01a47a0 100644 --- a/code/using_GO/pla/T17_8_1_1000.R +++ b/code/using_GO/pla/T17_8_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_8_2001_3000.R b/code/using_GO/pla/T17_8_2001_3000.R index d35a28baab8302c4617a261349a6d40e6b258a78..957b53201cf7a43c36ce1ba3fd1cc1f532fa8149 100644 --- a/code/using_GO/pla/T17_8_2001_3000.R +++ b/code/using_GO/pla/T17_8_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_8_3001_4000.R b/code/using_GO/pla/T17_8_3001_4000.R index 97ac630d1164fc90c5db0bbe321af69606c87edf..52f95be59649bf88087e83a44580ee506322db56 100644 --- a/code/using_GO/pla/T17_8_3001_4000.R +++ b/code/using_GO/pla/T17_8_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_8_4001_5000.R b/code/using_GO/pla/T17_8_4001_5000.R index 343dbb0d7faf42f8de3ccc856a54b16e30516c7d..656a0cfd6c2e101db84e4113616d805a76965a45 100644 --- a/code/using_GO/pla/T17_8_4001_5000.R +++ b/code/using_GO/pla/T17_8_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_8_5001_6000.R b/code/using_GO/pla/T17_8_5001_6000.R index 0cef780146ba019f9513bb5f34d3bc443ab38763..6b1bb26d98c8b7cfa448e38cab71dc2ebc6fc126 100644 --- a/code/using_GO/pla/T17_8_5001_6000.R +++ b/code/using_GO/pla/T17_8_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T17_8_6001_7297.R b/code/using_GO/pla/T17_8_6001_7297.R index a4331119f9610956ae6845ab1c7eb8741662db89..e422447a1eb8fd3d1ef69e8c28d3121be37dc2c9 100644 --- a/code/using_GO/pla/T17_8_6001_7297.R +++ b/code/using_GO/pla/T17_8_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T17_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_1_1001_2000.R b/code/using_GO/pla/T18_1_1001_2000.R index e395a94945591c4132e3115e80d431661c6bb029..3d15255a5d3ca7bb53e07d66256a1037735f04ae 100644 --- a/code/using_GO/pla/T18_1_1001_2000.R +++ b/code/using_GO/pla/T18_1_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_1_1_1000.R b/code/using_GO/pla/T18_1_1_1000.R index aa48c3ceb48f7a348b13f9f972a901c7c4ad302b..19846189d78b1efc6755122e8ca6b1570867c66b 100644 --- a/code/using_GO/pla/T18_1_1_1000.R +++ b/code/using_GO/pla/T18_1_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_1_2001_3000.R b/code/using_GO/pla/T18_1_2001_3000.R index 8cc1b225c70b18b4ea4d1a60c36ade177b0cabf5..eec0015c3d0328b343c3a29758a38a5387aa3ddc 100644 --- a/code/using_GO/pla/T18_1_2001_3000.R +++ b/code/using_GO/pla/T18_1_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_1_3001_4000.R b/code/using_GO/pla/T18_1_3001_4000.R index bbd0e59db229f025f5288d00699117ecc9d72785..81459db214f77440a8a6f59d5cf13e7e9bee2c8f 100644 --- a/code/using_GO/pla/T18_1_3001_4000.R +++ b/code/using_GO/pla/T18_1_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_1_4001_5000.R b/code/using_GO/pla/T18_1_4001_5000.R index 0020d413a1a8cf7e983657610686edfdb20fb87c..3c367ff108a6c6ce99a97a65a06cb169c2e17106 100644 --- a/code/using_GO/pla/T18_1_4001_5000.R +++ b/code/using_GO/pla/T18_1_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_1_5001_6000.R b/code/using_GO/pla/T18_1_5001_6000.R index 21fb218cd14e6a2b0fef80e340f7c9d23f53ad67..ce134bb4b65711bc83faa1a75acca870fe11c224 100644 --- a/code/using_GO/pla/T18_1_5001_6000.R +++ b/code/using_GO/pla/T18_1_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_1_6001_7297.R b/code/using_GO/pla/T18_1_6001_7297.R index f9bbf65690548739a0759054cd35fe5065696bf5..409c3eb53b403fbdbc780e9c65bd7bd9732f1588 100644 --- a/code/using_GO/pla/T18_1_6001_7297.R +++ b/code/using_GO/pla/T18_1_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_2_1001_2000.R b/code/using_GO/pla/T18_2_1001_2000.R index 49d59796cd38ce9902a9bf6e18895c393d8e2b76..3a1a699e9ed987ca916b9973bedd33a658af245e 100644 --- a/code/using_GO/pla/T18_2_1001_2000.R +++ b/code/using_GO/pla/T18_2_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_2_1_1000.R b/code/using_GO/pla/T18_2_1_1000.R index a33fe9d6dffd3d5405c7614164318516a1a2d199..7ec0f92124d6d2add17b799232353830d28b5366 100644 --- a/code/using_GO/pla/T18_2_1_1000.R +++ b/code/using_GO/pla/T18_2_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_2_2001_3000.R b/code/using_GO/pla/T18_2_2001_3000.R index b69edc8cab2313b7f1ef4870a12a1f850c01b0e8..cd1d13e085ada9c3cf02de5db0ed1856754ed94b 100644 --- a/code/using_GO/pla/T18_2_2001_3000.R +++ b/code/using_GO/pla/T18_2_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_2_3001_4000.R b/code/using_GO/pla/T18_2_3001_4000.R index a29a303ce22016aebba0daee2e10209077fe9864..e82c87b3cbe96bfed92ab16e7c8b5bc682858269 100644 --- a/code/using_GO/pla/T18_2_3001_4000.R +++ b/code/using_GO/pla/T18_2_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_2_4001_5000.R b/code/using_GO/pla/T18_2_4001_5000.R index 239fdb6777ffa2b23dc730fefbbfb7fe447b8dcc..a379f08431b783c54dcd2d22b2b20e91aa1cf641 100644 --- a/code/using_GO/pla/T18_2_4001_5000.R +++ b/code/using_GO/pla/T18_2_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_2_5001_6000.R b/code/using_GO/pla/T18_2_5001_6000.R index 95143f44b9bb7945cf245feaa814c9bedc53590c..078e0201135c7d1671098d8a6026dde524f4abae 100644 --- a/code/using_GO/pla/T18_2_5001_6000.R +++ b/code/using_GO/pla/T18_2_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_2_6001_7297.R b/code/using_GO/pla/T18_2_6001_7297.R index 8d7216d25c2814e6424316f2839dbf19a1a9c434..b352c2faa024dc95cc3b3de4c4d64491ab8c2009 100644 --- a/code/using_GO/pla/T18_2_6001_7297.R +++ b/code/using_GO/pla/T18_2_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_3_1001_2000.R b/code/using_GO/pla/T18_3_1001_2000.R index 5e541d70ee4202343ed808b6cc48c87b73f5a749..7267804e511a7cbe28982a9c62423ea3f082c99a 100644 --- a/code/using_GO/pla/T18_3_1001_2000.R +++ b/code/using_GO/pla/T18_3_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_3_1_1000.R b/code/using_GO/pla/T18_3_1_1000.R index 5a282084c814e34ea42088524b2f629ea3701672..4c135b8a51eead6eafe7a1b87f25df3187dad331 100644 --- a/code/using_GO/pla/T18_3_1_1000.R +++ b/code/using_GO/pla/T18_3_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_3_2001_3000.R b/code/using_GO/pla/T18_3_2001_3000.R index d1d57df1adbda0f27d791504ad045d84b7f9b0e1..0e1497670b7f3846817eb3a55b33908f12778385 100644 --- a/code/using_GO/pla/T18_3_2001_3000.R +++ b/code/using_GO/pla/T18_3_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_3_3001_4000.R b/code/using_GO/pla/T18_3_3001_4000.R index 72091067c772ad9cc3bdfd254fcccd23a619e522..387fcf742fcd39da2fb5e696c8aeaedf6c88424b 100644 --- a/code/using_GO/pla/T18_3_3001_4000.R +++ b/code/using_GO/pla/T18_3_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_3_4001_5000.R b/code/using_GO/pla/T18_3_4001_5000.R index 600b5b1449fed4716bf191ef73186da6108d9649..abc2365ecfc8e983ec947c89dc276273eec862e1 100644 --- a/code/using_GO/pla/T18_3_4001_5000.R +++ b/code/using_GO/pla/T18_3_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_3_5001_6000.R b/code/using_GO/pla/T18_3_5001_6000.R index dddf977f5b05340725b2e912d810bb09256e1572..27cd69807ef6aac71eea1658f398d9cb4a799c41 100644 --- a/code/using_GO/pla/T18_3_5001_6000.R +++ b/code/using_GO/pla/T18_3_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_3_6001_7297.R b/code/using_GO/pla/T18_3_6001_7297.R index b2ad2ebf1ed898e34a2106abddd55e6489a42406..f54c0d93748463e85cc233b01ca1b98d0513953f 100644 --- a/code/using_GO/pla/T18_3_6001_7297.R +++ b/code/using_GO/pla/T18_3_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_4_1001_2000.R b/code/using_GO/pla/T18_4_1001_2000.R index f3f2b966d757b27eefb5fb7ec228c66ffa0a82e2..55a008c1104d0d9ec9f5c1f58355e5f7502a1c44 100644 --- a/code/using_GO/pla/T18_4_1001_2000.R +++ b/code/using_GO/pla/T18_4_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_4_1_1000.R b/code/using_GO/pla/T18_4_1_1000.R index 287f78496dc7f57b161308fe6e0495c7b0aedb2d..3fa26c6fea069c81d9c848df1f5f317753233a9e 100644 --- a/code/using_GO/pla/T18_4_1_1000.R +++ b/code/using_GO/pla/T18_4_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_4_2001_3000.R b/code/using_GO/pla/T18_4_2001_3000.R index c6212a6b706873501508c259ee6ece5b4261df83..e7befd58e4bbffd8cf47e32bff00aeb7454a4a47 100644 --- a/code/using_GO/pla/T18_4_2001_3000.R +++ b/code/using_GO/pla/T18_4_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_4_3001_4000.R b/code/using_GO/pla/T18_4_3001_4000.R index 33598de71b91621e62d8c1e7197d10e20702ac3e..84beee87055ae670deefc674c0f772bfca03ed7a 100644 --- a/code/using_GO/pla/T18_4_3001_4000.R +++ b/code/using_GO/pla/T18_4_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_4_4001_5000.R b/code/using_GO/pla/T18_4_4001_5000.R index 1dbce5c463b1e63407e0a24364df883503ac4450..c5affc98fa1fe06edaf0106e33f773d9742cf8ec 100644 --- a/code/using_GO/pla/T18_4_4001_5000.R +++ b/code/using_GO/pla/T18_4_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_4_5001_6000.R b/code/using_GO/pla/T18_4_5001_6000.R index ec1a8a0af02f27f8631d2738ad973f33ecbd60d7..d1d82bda8e277cea09b845bd9cbdfd5f55306359 100644 --- a/code/using_GO/pla/T18_4_5001_6000.R +++ b/code/using_GO/pla/T18_4_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_4_6001_7297.R b/code/using_GO/pla/T18_4_6001_7297.R index 3827199cafeb0c927dbd19d30028cec227f205fd..0fdc0102e2fa4abf8898873352db640ec05be074 100644 --- a/code/using_GO/pla/T18_4_6001_7297.R +++ b/code/using_GO/pla/T18_4_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_5_1001_2000.R b/code/using_GO/pla/T18_5_1001_2000.R index 26fcb78f1fef98e5f82b7272b0e49d9ebfe86ef0..235a3d831faf666e10c6951ddfdd3051c672003c 100644 --- a/code/using_GO/pla/T18_5_1001_2000.R +++ b/code/using_GO/pla/T18_5_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_5_1_1000.R b/code/using_GO/pla/T18_5_1_1000.R index 0a360771122e65b70abe82699e5aed382afb62a0..599c702b328e85fce78ac1f2ab5b68cca271ccf2 100644 --- a/code/using_GO/pla/T18_5_1_1000.R +++ b/code/using_GO/pla/T18_5_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_5_2001_3000.R b/code/using_GO/pla/T18_5_2001_3000.R index 29dead93539296308de441985fdb331c4a9880a5..f2743ffc39ecedbffa342ea457400a7528e5326a 100644 --- a/code/using_GO/pla/T18_5_2001_3000.R +++ b/code/using_GO/pla/T18_5_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_5_3001_4000.R b/code/using_GO/pla/T18_5_3001_4000.R index 4b7e1ad297bb1ea4412cf903aacc949a5d7bbcb5..ad4ecf80ab1af470f132ddfa7813246b0805a81a 100644 --- a/code/using_GO/pla/T18_5_3001_4000.R +++ b/code/using_GO/pla/T18_5_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_5_4001_5000.R b/code/using_GO/pla/T18_5_4001_5000.R index 97e3b412ea2446d1262abdd9fb13e8678fd78bbe..3b2d3b623785fcb990948dab37dfdc3f7fea2bd9 100644 --- a/code/using_GO/pla/T18_5_4001_5000.R +++ b/code/using_GO/pla/T18_5_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_5_5001_6000.R b/code/using_GO/pla/T18_5_5001_6000.R index 7983d5c88cf422b592513a162cb80e79bf464b6b..3f7d95139f89fb05c009322f01597ef3b58990c9 100644 --- a/code/using_GO/pla/T18_5_5001_6000.R +++ b/code/using_GO/pla/T18_5_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_5_6001_7297.R b/code/using_GO/pla/T18_5_6001_7297.R index e08624495c4ff93d23df8920040fc46563b8da6b..33a8aa9d68668cc8032d9b115bb62843dfae2b01 100644 --- a/code/using_GO/pla/T18_5_6001_7297.R +++ b/code/using_GO/pla/T18_5_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_6_1001_2000.R b/code/using_GO/pla/T18_6_1001_2000.R index 19a770a612880401f4288c0b57637f84dc2d5c4f..8b11dbe2652404712bbf2af33a4978ba91b5e493 100644 --- a/code/using_GO/pla/T18_6_1001_2000.R +++ b/code/using_GO/pla/T18_6_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_6_1_1000.R b/code/using_GO/pla/T18_6_1_1000.R index 5793c29bbe8ce2ef853350554c1161f7327d52aa..59dc1e9e49b234a9c048c49d9ddb996b8e3e9b22 100644 --- a/code/using_GO/pla/T18_6_1_1000.R +++ b/code/using_GO/pla/T18_6_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_6_2001_3000.R b/code/using_GO/pla/T18_6_2001_3000.R index dc17a9ec4e97d0e735db69eff0397cfdd8001412..19682ac86d8a5cdd59da0601361f46e0c21b2f7b 100644 --- a/code/using_GO/pla/T18_6_2001_3000.R +++ b/code/using_GO/pla/T18_6_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_6_3001_4000.R b/code/using_GO/pla/T18_6_3001_4000.R index 7c305d444e635ebb2cff071153ecddf0a266056d..f7dba2e80cd29d02d1c752f340633265d1473200 100644 --- a/code/using_GO/pla/T18_6_3001_4000.R +++ b/code/using_GO/pla/T18_6_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_6_4001_5000.R b/code/using_GO/pla/T18_6_4001_5000.R index fd400b753f410380d5d15ebde9fa45ac7f10078b..52e7348473d05c750d9617431eea206ab541023a 100644 --- a/code/using_GO/pla/T18_6_4001_5000.R +++ b/code/using_GO/pla/T18_6_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_6_5001_6000.R b/code/using_GO/pla/T18_6_5001_6000.R index 6016036de8e1a7e6fa298d0ce4f543c8465f49a0..93cd5c5460912c169f281461270ee9e7ef8f7c52 100644 --- a/code/using_GO/pla/T18_6_5001_6000.R +++ b/code/using_GO/pla/T18_6_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_6_6001_7297.R b/code/using_GO/pla/T18_6_6001_7297.R index 32ed66721ec64fc413fed41ce12cce62b8004bb3..718cbd1773c70c94bd788a815872fc9a12d770fe 100644 --- a/code/using_GO/pla/T18_6_6001_7297.R +++ b/code/using_GO/pla/T18_6_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_7_1001_2000.R b/code/using_GO/pla/T18_7_1001_2000.R index 12d6413c2e2ae46fb21ae9b36430fb62825551e8..1236569e4f6fd91565bd01575b01c36b7494f88a 100644 --- a/code/using_GO/pla/T18_7_1001_2000.R +++ b/code/using_GO/pla/T18_7_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_7_1_1000.R b/code/using_GO/pla/T18_7_1_1000.R index 160483dc9a120ef40a70b3cac03d8ec59dc8e1e1..5b2dc02a708f742e371bfe6ecf250e2e26e02354 100644 --- a/code/using_GO/pla/T18_7_1_1000.R +++ b/code/using_GO/pla/T18_7_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_7_2001_3000.R b/code/using_GO/pla/T18_7_2001_3000.R index 8a7325564813bdb7314bf1230b7028c7edaa92ff..499fe044d53d331537085649b69970699980411d 100644 --- a/code/using_GO/pla/T18_7_2001_3000.R +++ b/code/using_GO/pla/T18_7_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_7_3001_4000.R b/code/using_GO/pla/T18_7_3001_4000.R index 24a77c8bad8c5c2012b711fab61877bb787e89bb..9be5a1fcafd059d21bb1b5de067e3ee3d9d4ce06 100644 --- a/code/using_GO/pla/T18_7_3001_4000.R +++ b/code/using_GO/pla/T18_7_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_7_4001_5000.R b/code/using_GO/pla/T18_7_4001_5000.R index eb76ec90bd7a7ac6000f69a79a455455d45d5627..1e805e372117b8a441ef3184a2cb291e8b15fd73 100644 --- a/code/using_GO/pla/T18_7_4001_5000.R +++ b/code/using_GO/pla/T18_7_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_7_5001_6000.R b/code/using_GO/pla/T18_7_5001_6000.R index eb898ff1f296d41f1bf34626fce63f072a6e2926..10bea6c0c8412585bf955c44a385e45db3f0fd2c 100644 --- a/code/using_GO/pla/T18_7_5001_6000.R +++ b/code/using_GO/pla/T18_7_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_7_6001_7297.R b/code/using_GO/pla/T18_7_6001_7297.R index 8d9de369233dc701474fa4bcd50b85086ca085aa..a7c8db8ed47508a54ac358f3d9d673fa4122dd24 100644 --- a/code/using_GO/pla/T18_7_6001_7297.R +++ b/code/using_GO/pla/T18_7_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_8_1001_2000.R b/code/using_GO/pla/T18_8_1001_2000.R index 198b00754dc71963b989cacb6f0e9dd877f2ed59..cf9db30451b1602787a0a89e969859e1b264d490 100644 --- a/code/using_GO/pla/T18_8_1001_2000.R +++ b/code/using_GO/pla/T18_8_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_8_1_1000.R b/code/using_GO/pla/T18_8_1_1000.R index bce9d22f7f8bd15a9e8d18b57bf67c5f3c8b2d86..5d77d1f5b6643bc2adbf3cfec23bf38099f2cdb1 100644 --- a/code/using_GO/pla/T18_8_1_1000.R +++ b/code/using_GO/pla/T18_8_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_8_2001_3000.R b/code/using_GO/pla/T18_8_2001_3000.R index 627207793e3585760670d83f6a106dc79a3044a2..d21531a4484bd64cb44879472c08175f5d2912ea 100644 --- a/code/using_GO/pla/T18_8_2001_3000.R +++ b/code/using_GO/pla/T18_8_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_8_3001_4000.R b/code/using_GO/pla/T18_8_3001_4000.R index 5f09c0327bed99049ecd32ab39e125996ddc87d6..43bd8fdd213d210fb90baa47cda6fa7688f5a2fb 100644 --- a/code/using_GO/pla/T18_8_3001_4000.R +++ b/code/using_GO/pla/T18_8_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_8_4001_5000.R b/code/using_GO/pla/T18_8_4001_5000.R index 9b870c8767efb1291a0aed465fb3ecd7c3283026..d5dd96dcbed6e872b8c0ff40bb0da00061b4fdd6 100644 --- a/code/using_GO/pla/T18_8_4001_5000.R +++ b/code/using_GO/pla/T18_8_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_8_5001_6000.R b/code/using_GO/pla/T18_8_5001_6000.R index efe52ac7ee7cffc3a1afbbd71a94d4402dc82d8b..9e29a3dfda3f14208812302373ce14068dc760c1 100644 --- a/code/using_GO/pla/T18_8_5001_6000.R +++ b/code/using_GO/pla/T18_8_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T18_8_6001_7297.R b/code/using_GO/pla/T18_8_6001_7297.R index e91b2ed9a6f09859a1ff3b5fdc6912d0d86b3a5f..83c1e61a9a4ae086c48de5606436a457ff995bbf 100644 --- a/code/using_GO/pla/T18_8_6001_7297.R +++ b/code/using_GO/pla/T18_8_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T18_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_1_1001_2000.R b/code/using_GO/pla/T19_1_1001_2000.R index a24d3bd166260892d6f4e367c17f711bb58c6e82..401278986e3492c04899d2b856fdc500a21b5020 100644 --- a/code/using_GO/pla/T19_1_1001_2000.R +++ b/code/using_GO/pla/T19_1_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_1_1_1000.R b/code/using_GO/pla/T19_1_1_1000.R index df74bb6b4a633d233523d30d52912d9eba294bb8..075cdb92fd7c4e4e9883a34cfb8f11fb9b9babcf 100644 --- a/code/using_GO/pla/T19_1_1_1000.R +++ b/code/using_GO/pla/T19_1_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_1_2001_3000.R b/code/using_GO/pla/T19_1_2001_3000.R index 9993149fcd1f7911c8ed88171c7a7c62145569f0..53ba19033e98586a322cb919c92403136d3b2bb8 100644 --- a/code/using_GO/pla/T19_1_2001_3000.R +++ b/code/using_GO/pla/T19_1_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_1_3001_4000.R b/code/using_GO/pla/T19_1_3001_4000.R index 3acc5e88a6c6d613933e4571feacafe955b1f823..83b46773e9aaf84eae0aeb87107bb32a05e18e7c 100644 --- a/code/using_GO/pla/T19_1_3001_4000.R +++ b/code/using_GO/pla/T19_1_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_1_4001_5000.R b/code/using_GO/pla/T19_1_4001_5000.R index c1f73901b2550978ac8b9cdbfea8074946653cc1..b153928ca0b49f9265e7a2f2404052b02329018c 100644 --- a/code/using_GO/pla/T19_1_4001_5000.R +++ b/code/using_GO/pla/T19_1_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_1_5001_6000.R b/code/using_GO/pla/T19_1_5001_6000.R index 43fe40c6f9cca70c02e91c4ff32e548990ce945f..635bff564ecfecbc6e4b20bef85ba6acce673b8c 100644 --- a/code/using_GO/pla/T19_1_5001_6000.R +++ b/code/using_GO/pla/T19_1_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_1_6001_7297.R b/code/using_GO/pla/T19_1_6001_7297.R index b5653add1576ec7a8910169c6218f82ac5bab913..d0fb5c15b0bf80ca274ca01e8e11b1224d6b82ce 100644 --- a/code/using_GO/pla/T19_1_6001_7297.R +++ b/code/using_GO/pla/T19_1_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_2_1001_2000.R b/code/using_GO/pla/T19_2_1001_2000.R index 32966c178b82e9c40c21bb3b4cf8a692a4d6bccb..eb9a0e1f2ad602fe003caba279ad69286ed24fc9 100644 --- a/code/using_GO/pla/T19_2_1001_2000.R +++ b/code/using_GO/pla/T19_2_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_2_1_1000.R b/code/using_GO/pla/T19_2_1_1000.R index 6921cb1b1c5801b1319ba87ec98499cfd921da90..a96c3f04ec00f25daf7259705d01a94e8af787db 100644 --- a/code/using_GO/pla/T19_2_1_1000.R +++ b/code/using_GO/pla/T19_2_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_2_2001_3000.R b/code/using_GO/pla/T19_2_2001_3000.R index dd72470e7fe5571e2737de39c3567b067275e4b0..d3710a75677ac2a6d5ba0aa6005d7c2bc595e322 100644 --- a/code/using_GO/pla/T19_2_2001_3000.R +++ b/code/using_GO/pla/T19_2_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_2_3001_4000.R b/code/using_GO/pla/T19_2_3001_4000.R index 37815c874f15808ce45ac6c84ff8ca4441cba316..c7fae60aab9fd40429f2caabb04024f6851a1117 100644 --- a/code/using_GO/pla/T19_2_3001_4000.R +++ b/code/using_GO/pla/T19_2_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_2_4001_5000.R b/code/using_GO/pla/T19_2_4001_5000.R index 086a394dce42794b480fe4177f174a4ce4fc24ce..f6ff6a5061a788fed91c71bc108cd628e52f30d6 100644 --- a/code/using_GO/pla/T19_2_4001_5000.R +++ b/code/using_GO/pla/T19_2_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_2_5001_6000.R b/code/using_GO/pla/T19_2_5001_6000.R index 7633b44c485756bc2c8e7f733db4e0a25d9ea491..fccf2f74e7f71295866512ad2f4be556e330d340 100644 --- a/code/using_GO/pla/T19_2_5001_6000.R +++ b/code/using_GO/pla/T19_2_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_2_6001_7297.R b/code/using_GO/pla/T19_2_6001_7297.R index 76fed4e3dadf108ee2cd6b4aed38562e3d5b5738..a2af490cd5d4bac61328c6372ad2413d62189060 100644 --- a/code/using_GO/pla/T19_2_6001_7297.R +++ b/code/using_GO/pla/T19_2_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_3_1001_2000.R b/code/using_GO/pla/T19_3_1001_2000.R index 157a4b4e595cb3f08938ecb1afe5cab9f8aa707f..fbd925cf2bd4564f824f45797ddb2b92eed4ca0a 100644 --- a/code/using_GO/pla/T19_3_1001_2000.R +++ b/code/using_GO/pla/T19_3_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_3_1_1000.R b/code/using_GO/pla/T19_3_1_1000.R index 692b82387919766ac5526c330f5925020ea8b02d..aefa6e784de5e6940179294be2bef3ccabd41bd9 100644 --- a/code/using_GO/pla/T19_3_1_1000.R +++ b/code/using_GO/pla/T19_3_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_3_2001_3000.R b/code/using_GO/pla/T19_3_2001_3000.R index 8962a1d60df3a467c5dbcd3d1340227b6404dc14..9199651b3a8267efc486a1d39741dcc6bdb2c6b2 100644 --- a/code/using_GO/pla/T19_3_2001_3000.R +++ b/code/using_GO/pla/T19_3_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_3_3001_4000.R b/code/using_GO/pla/T19_3_3001_4000.R index e09750c406019d179a97a7bc6e4f054f4a93d497..d2d86f3bab8301617a37954c6865ad68fa7dcd91 100644 --- a/code/using_GO/pla/T19_3_3001_4000.R +++ b/code/using_GO/pla/T19_3_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_3_4001_5000.R b/code/using_GO/pla/T19_3_4001_5000.R index 8daf7777c507c04b5a8fb5a7455fd0154243e165..0138bc7409503a88188aa585944e170917e5301b 100644 --- a/code/using_GO/pla/T19_3_4001_5000.R +++ b/code/using_GO/pla/T19_3_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_3_5001_6000.R b/code/using_GO/pla/T19_3_5001_6000.R index 4305ce8022d3fe8359d9a7a68eab2197ed858b20..54d5b56ce6d3f4d4ae6beb13d2d45996a0f6be12 100644 --- a/code/using_GO/pla/T19_3_5001_6000.R +++ b/code/using_GO/pla/T19_3_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_3_6001_7297.R b/code/using_GO/pla/T19_3_6001_7297.R index ade8f192bec890c67a136193234ca192cc20a318..57b0788b4fe4caf4d209b476eda6453fa4a1330c 100644 --- a/code/using_GO/pla/T19_3_6001_7297.R +++ b/code/using_GO/pla/T19_3_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_3_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_4_1001_2000.R b/code/using_GO/pla/T19_4_1001_2000.R index afebbb4585d0de8144367ab0280502df523233c1..8b04bd9c4f9c6d3d905a4f21e260a51404788053 100644 --- a/code/using_GO/pla/T19_4_1001_2000.R +++ b/code/using_GO/pla/T19_4_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_4_1_1000.R b/code/using_GO/pla/T19_4_1_1000.R index 2e215a577fd34c14209bd7c713918b0e6e90f5ee..51503d084d6b12692e601bc3d872eb5a865ad960 100644 --- a/code/using_GO/pla/T19_4_1_1000.R +++ b/code/using_GO/pla/T19_4_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_4_2001_3000.R b/code/using_GO/pla/T19_4_2001_3000.R index 729ace8d7ca07567d6c6295f7eaa60a191b37c7a..349dc218d825aa76f339c14b2d72f804242d85c8 100644 --- a/code/using_GO/pla/T19_4_2001_3000.R +++ b/code/using_GO/pla/T19_4_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_4_3001_4000.R b/code/using_GO/pla/T19_4_3001_4000.R index 6bf9e07e018aef058532b898006016d61388f473..79ac4e9981119eca0305690d53691f8d08a019ad 100644 --- a/code/using_GO/pla/T19_4_3001_4000.R +++ b/code/using_GO/pla/T19_4_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_4_4001_5000.R b/code/using_GO/pla/T19_4_4001_5000.R index 5686a5e76cf01e857ebdb3598eaf20dd1b727fa0..6870955e7b61ae4ae44086739bf8513ce2ee7d22 100644 --- a/code/using_GO/pla/T19_4_4001_5000.R +++ b/code/using_GO/pla/T19_4_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_4_5001_6000.R b/code/using_GO/pla/T19_4_5001_6000.R index 5917ed4ee6dcbd64b2fa7d99366e8ce768e49d66..c894e02a8c672966af50b888e69791bf2c7bab79 100644 --- a/code/using_GO/pla/T19_4_5001_6000.R +++ b/code/using_GO/pla/T19_4_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_4_6001_7297.R b/code/using_GO/pla/T19_4_6001_7297.R index 815713095d8ed4997a4c3b337da1aa16e769bd49..721057e2b3c900293983a3c257ce5e9eee761e86 100644 --- a/code/using_GO/pla/T19_4_6001_7297.R +++ b/code/using_GO/pla/T19_4_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_4_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_5_1001_2000.R b/code/using_GO/pla/T19_5_1001_2000.R index d45a19959af561dc3872c9d624749328c5151ca7..edae8dde73fcd16d0b5a76a575be2034d7861a9b 100644 --- a/code/using_GO/pla/T19_5_1001_2000.R +++ b/code/using_GO/pla/T19_5_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_5_1_1000.R b/code/using_GO/pla/T19_5_1_1000.R index f5ff7ca4174bf7eadf94c8fe06e394d1f717516f..a9d892389bbdb8826faaae69e34a984811026173 100644 --- a/code/using_GO/pla/T19_5_1_1000.R +++ b/code/using_GO/pla/T19_5_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_5_2001_3000.R b/code/using_GO/pla/T19_5_2001_3000.R index 357aafd29d11c4663a4ae0ec844adb0f8d124b19..0e693b413f7caf855e9743fb0aad5d2e0a6dda20 100644 --- a/code/using_GO/pla/T19_5_2001_3000.R +++ b/code/using_GO/pla/T19_5_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_5_3001_4000.R b/code/using_GO/pla/T19_5_3001_4000.R index 8d1ab5c5547e07d0b0dc1e231312fc62b33afc01..2af97cd0a7267e890a42cd334b3708a11bfb4efd 100644 --- a/code/using_GO/pla/T19_5_3001_4000.R +++ b/code/using_GO/pla/T19_5_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_5_4001_5000.R b/code/using_GO/pla/T19_5_4001_5000.R index af4cb87b7baa904f54a8065411af1864afffae65..a62ddf3b967e91d9c8b92011a512684c3a403f2b 100644 --- a/code/using_GO/pla/T19_5_4001_5000.R +++ b/code/using_GO/pla/T19_5_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_5_5001_6000.R b/code/using_GO/pla/T19_5_5001_6000.R index 3c1a372e0fd25b5f3115040d4dbacc2af2def03f..aa285dc2a6fafa09c5fe6c335ea0d0b0b28e3a9e 100644 --- a/code/using_GO/pla/T19_5_5001_6000.R +++ b/code/using_GO/pla/T19_5_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_5_6001_7297.R b/code/using_GO/pla/T19_5_6001_7297.R index f6970dbf1cbc8d79ec997d3c248366387c171167..283aa3ab3bcec4521356e9cde493ecbd6b36513a 100644 --- a/code/using_GO/pla/T19_5_6001_7297.R +++ b/code/using_GO/pla/T19_5_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_5_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_6_1001_2000.R b/code/using_GO/pla/T19_6_1001_2000.R index 0b6396ceb5b1c8318e1fa9c31c30acdb467863fb..9c4755f9f38f7f228d28e54a093a6b1dac217a78 100644 --- a/code/using_GO/pla/T19_6_1001_2000.R +++ b/code/using_GO/pla/T19_6_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_6_1_1000.R b/code/using_GO/pla/T19_6_1_1000.R index 4962934c14873d393da1487e42f55ecf6556f3e7..fe92f7dd125ea04340c8ead097bc44c50389149a 100644 --- a/code/using_GO/pla/T19_6_1_1000.R +++ b/code/using_GO/pla/T19_6_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_6_2001_3000.R b/code/using_GO/pla/T19_6_2001_3000.R index e89602d8da75f5732d716770d73c7246c3ad7245..49091aa39289acfc5c9130016e040f03412b9432 100644 --- a/code/using_GO/pla/T19_6_2001_3000.R +++ b/code/using_GO/pla/T19_6_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_6_3001_4000.R b/code/using_GO/pla/T19_6_3001_4000.R index 6abad1e41c4ec7a334f2b9091c9560620c97013b..696be87bb531e0fa296fdae920d23d9ce48e7a75 100644 --- a/code/using_GO/pla/T19_6_3001_4000.R +++ b/code/using_GO/pla/T19_6_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_6_4001_5000.R b/code/using_GO/pla/T19_6_4001_5000.R index de6adc40d9a62e0d5bd7e55806401f20947c24f9..5592ea6665243a3bd21448d5b896593664d7abb5 100644 --- a/code/using_GO/pla/T19_6_4001_5000.R +++ b/code/using_GO/pla/T19_6_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_6_5001_6000.R b/code/using_GO/pla/T19_6_5001_6000.R index 9af25ae712cfb5423596b89dec19fba8a67d7683..8d3f5882422d31b20e697c0c117c36aa0d81ef65 100644 --- a/code/using_GO/pla/T19_6_5001_6000.R +++ b/code/using_GO/pla/T19_6_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_6_6001_7297.R b/code/using_GO/pla/T19_6_6001_7297.R index 06492fbb080c9a8e6c0787fc78098a97b648cc34..c98cce2050810feaf6d7658dda223fbccfeb1330 100644 --- a/code/using_GO/pla/T19_6_6001_7297.R +++ b/code/using_GO/pla/T19_6_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_6_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_7_1001_2000.R b/code/using_GO/pla/T19_7_1001_2000.R index c8d6c1079382cf341edf2a2cf26284f1ad1d2b05..cf36af378081a88ecd002884b4142beed6d9626f 100644 --- a/code/using_GO/pla/T19_7_1001_2000.R +++ b/code/using_GO/pla/T19_7_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_7_1_1000.R b/code/using_GO/pla/T19_7_1_1000.R index 450a7eff1b5451aa50fce66128896a1797a4d483..e48d3e7641f6b49143dea83875dc890d31317a4d 100644 --- a/code/using_GO/pla/T19_7_1_1000.R +++ b/code/using_GO/pla/T19_7_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_7_2001_3000.R b/code/using_GO/pla/T19_7_2001_3000.R index 7cb6b035793a1573cdd0dfcf6ad1ecbfb77cb785..4e2b8edadd6fc8ab5c8374bc8193209e5fe5104b 100644 --- a/code/using_GO/pla/T19_7_2001_3000.R +++ b/code/using_GO/pla/T19_7_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_7_3001_4000.R b/code/using_GO/pla/T19_7_3001_4000.R index bffea958b6da431f0812d3b3b676d7cb5e9803b1..eda96dae95620c16474bf004470159d2ffdbfb04 100644 --- a/code/using_GO/pla/T19_7_3001_4000.R +++ b/code/using_GO/pla/T19_7_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_7_4001_5000.R b/code/using_GO/pla/T19_7_4001_5000.R index f3ff4840a079ca1345b40f135826f5585643a7e3..1b91da246382823da964f04648b8f79ab9a2539f 100644 --- a/code/using_GO/pla/T19_7_4001_5000.R +++ b/code/using_GO/pla/T19_7_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_7_5001_6000.R b/code/using_GO/pla/T19_7_5001_6000.R index 0d79810fe228a1158b7d596d42bacfc624c31b40..d496d983cf1f5d12a1ae576663b917f3a18e2176 100644 --- a/code/using_GO/pla/T19_7_5001_6000.R +++ b/code/using_GO/pla/T19_7_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_7_6001_7297.R b/code/using_GO/pla/T19_7_6001_7297.R index 9d812e29e7c2d6990a64419280e9fddcec377dfb..dcd1945e5c81a9383fef127da8491367e9136239 100644 --- a/code/using_GO/pla/T19_7_6001_7297.R +++ b/code/using_GO/pla/T19_7_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_7_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_8_1001_2000.R b/code/using_GO/pla/T19_8_1001_2000.R index ea6b7916f5e09595fb6679f31cb858018c2e7063..5f5c01ed8d2f70acf12157f0b6335fdfc704d3b4 100644 --- a/code/using_GO/pla/T19_8_1001_2000.R +++ b/code/using_GO/pla/T19_8_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_8_1_1000.R b/code/using_GO/pla/T19_8_1_1000.R index e545504da5e34922c2ad97ad3a0bc15099ef735a..cec93bbb09b25494adf4b6630c5e6e3df0c55d7d 100644 --- a/code/using_GO/pla/T19_8_1_1000.R +++ b/code/using_GO/pla/T19_8_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_8_2001_3000.R b/code/using_GO/pla/T19_8_2001_3000.R index d87af76aa1c74fc86120f9156e98a219f14aa78c..b3e0edc018ec45ad73db8fa3f7f879dca0c283f1 100644 --- a/code/using_GO/pla/T19_8_2001_3000.R +++ b/code/using_GO/pla/T19_8_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_8_3001_4000.R b/code/using_GO/pla/T19_8_3001_4000.R index 9822cbc9db2e11b5b7e4735717fcab53d247e800..6f8b04de21b2c173d251f16bdeb1eb867f1bd733 100644 --- a/code/using_GO/pla/T19_8_3001_4000.R +++ b/code/using_GO/pla/T19_8_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_8_4001_5000.R b/code/using_GO/pla/T19_8_4001_5000.R index 4a5b40aecbfe6606ea24503b978d3eb8f43c4222..a6a8c95d7d1cd6bc869fccb0b9d6e17898f5fa2b 100644 --- a/code/using_GO/pla/T19_8_4001_5000.R +++ b/code/using_GO/pla/T19_8_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_8_5001_6000.R b/code/using_GO/pla/T19_8_5001_6000.R index 766d4f81b0fa5086fbf0ff4804dfff5a4b73c824..6a09d1425dcb9ffc97d61bc73d495cf4113271d3 100644 --- a/code/using_GO/pla/T19_8_5001_6000.R +++ b/code/using_GO/pla/T19_8_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T19_8_6001_7297.R b/code/using_GO/pla/T19_8_6001_7297.R index c699d860a2e2079b74edb4dabb954008a808e396..8a3e143270e0282a066e27066f0d707f9958e412 100644 --- a/code/using_GO/pla/T19_8_6001_7297.R +++ b/code/using_GO/pla/T19_8_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T19_8_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T20_1_1001_2000.R b/code/using_GO/pla/T20_1_1001_2000.R index e4f24a8d44f33e51f74abcac6a3feed5f7c331c7..2027d48db136ee9f92da03e8e9fdfb66ceba4076 100644 --- a/code/using_GO/pla/T20_1_1001_2000.R +++ b/code/using_GO/pla/T20_1_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T20_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T20_1_1_1000.R b/code/using_GO/pla/T20_1_1_1000.R index 7b0d3d309b085fc67b059d7f1a249271bd037898..b683a676ea7928f15cb68788eca29bb744c41bd2 100644 --- a/code/using_GO/pla/T20_1_1_1000.R +++ b/code/using_GO/pla/T20_1_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T20_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T20_1_2001_3000.R b/code/using_GO/pla/T20_1_2001_3000.R index dac8bf875a3904137245ddd3fd7ac8f6b8c3c3b1..8ab5747625ba6c347612c3148cde4a7fc3c0a4ae 100644 --- a/code/using_GO/pla/T20_1_2001_3000.R +++ b/code/using_GO/pla/T20_1_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T20_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T20_1_3001_4000.R b/code/using_GO/pla/T20_1_3001_4000.R index 789b0408307a6a86357880cc5e29f5d47e49ab17..c14f8a6e0d6d5acdf6b2bfb818b9c88b60c47e27 100644 --- a/code/using_GO/pla/T20_1_3001_4000.R +++ b/code/using_GO/pla/T20_1_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T20_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T20_1_4001_5000.R b/code/using_GO/pla/T20_1_4001_5000.R index 4a8b3569f6578ca7707be75bbec4f8dbe9d74b58..886391365c803d4e00d31f06fa9a0e48260688af 100644 --- a/code/using_GO/pla/T20_1_4001_5000.R +++ b/code/using_GO/pla/T20_1_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T20_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T20_1_5001_6000.R b/code/using_GO/pla/T20_1_5001_6000.R index ed86247cba37a5d990a5814781272cb68248a369..7228e438be83d755cc1f1d5a07164c9b8546fbcd 100644 --- a/code/using_GO/pla/T20_1_5001_6000.R +++ b/code/using_GO/pla/T20_1_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T20_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T20_1_6001_7297.R b/code/using_GO/pla/T20_1_6001_7297.R index ce3fb321b113a6385028404986490736c25e0007..b7df92032b64c9a8f99df9a15841aabc9338bb22 100644 --- a/code/using_GO/pla/T20_1_6001_7297.R +++ b/code/using_GO/pla/T20_1_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T20_1_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T20_2_1001_2000.R b/code/using_GO/pla/T20_2_1001_2000.R index 7242215366070f1b2fdac7973b1907dd87ca066d..6fe0f9124351a8ba4bc93be3cade0993d4ccfebf 100644 --- a/code/using_GO/pla/T20_2_1001_2000.R +++ b/code/using_GO/pla/T20_2_1001_2000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1001:2000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T20_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T20_2_1_1000.R b/code/using_GO/pla/T20_2_1_1000.R index ada4b08a2489a7ffd3c734b3fd643333580b5ee4..a376915c5e349365b71bd87710c9a17ca35abfb1 100644 --- a/code/using_GO/pla/T20_2_1_1000.R +++ b/code/using_GO/pla/T20_2_1_1000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[1:1000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T20_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T20_2_2001_3000.R b/code/using_GO/pla/T20_2_2001_3000.R index 5dbc48d887f2a520c231043bea2400c0c3d6fdea..b472badb385d9cefb49655d8b35912bd001dbdf6 100644 --- a/code/using_GO/pla/T20_2_2001_3000.R +++ b/code/using_GO/pla/T20_2_2001_3000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[2001:3000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T20_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T20_2_3001_4000.R b/code/using_GO/pla/T20_2_3001_4000.R index 0824607f931870331413cafff151ebb72ce1f7ad..82f45c03fa265c297c99b68f6781348c79767f6b 100644 --- a/code/using_GO/pla/T20_2_3001_4000.R +++ b/code/using_GO/pla/T20_2_3001_4000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[3001:4000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T20_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T20_2_4001_5000.R b/code/using_GO/pla/T20_2_4001_5000.R index fe263e253bb31f11edfe1e23cc8a755406ae67fd..a88e2bc4e065ed18795620ced0d8321ce49e3f9c 100644 --- a/code/using_GO/pla/T20_2_4001_5000.R +++ b/code/using_GO/pla/T20_2_4001_5000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[4001:5000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T20_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T20_2_5001_6000.R b/code/using_GO/pla/T20_2_5001_6000.R index d10b15090c0dacac64861e9b0197f3eebefac203..d7bedd423d93d6fe314ca7ebab98cb5007fa235f 100644 --- a/code/using_GO/pla/T20_2_5001_6000.R +++ b/code/using_GO/pla/T20_2_5001_6000.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[5001:6000] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T20_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/T20_2_6001_7297.R b/code/using_GO/pla/T20_2_6001_7297.R index 0b0f4751d0f8e8ffedd3804ba601068480f5f264..2b8eac68ceb2d4cb12ce29ad6c2aaf8584869542 100644 --- a/code/using_GO/pla/T20_2_6001_7297.R +++ b/code/using_GO/pla/T20_2_6001_7297.R @@ -8,7 +8,25 @@ is.installed <- function(mypkg) } ######################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} + +setwd(paste0(wdir,"/",wd,"/8old")); +######################################################################################## #if (!is.installed("backports")) #{ @@ -32,26 +50,26 @@ library('qgg') library('dplyr') ########################################################################################### message("Loading data...") -MAC_matrix_with_header=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_matrix_with_header.rds") -accessions=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/accessions.rds") -all_nucl_genes_bed=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/all_nucl_genes_bed.rds") -ath_all_new_maf_ldpruned_map=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/ath_all_new_maf_ldpruned_map.rds") -W=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/W.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/G.Rdata") -MAC_df=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/MAC_df.rds") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/Pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/geno_pheno_pla.Rdata") -load(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/data/pheno_df_pla.Rdata") -go_all_genes_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_genes_number.rds") #7432 -go_all_markers_number=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers_number.rds") #7432 -go_all_markers=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/go_all_markers.rds") #7432 -markerSets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/markerSets.rds") #7297 excluding those go terms with zero markers -setsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/setsGF.rds") #7297 excluding those go terms with zero markers -rsetsGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rsetsGF.rds") #7297 excluding those go terms with zero markers -nsets=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsets.rds") #7297 excluding those go terms with zero markers -nsnps=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/nsnps.rds") #7297 excluding those go terms with zero markers -GF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/GF.rds") #7297 excluding those go terms with zero markers -rGF=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/priors/go/rGF.rds") #7297 excluding those go terms with zero markers +MAC_matrix_with_header=readRDS(file="../../../../data/MAC_matrix_with_header.rds") +accessions=readRDS(file="../../../../data/accessions.rds") +all_nucl_genes_bed=readRDS(file="../../../../data/all_nucl_genes_bed.rds") +ath_all_new_maf_ldpruned_map=readRDS(file="../../../../data/ath_all_new_maf_ldpruned_map.rds") +W=readRDS(file="../../../../data/W.rds") +load(file="../../../../data/G.Rdata") +MAC_df=readRDS(file="../../../../data/MAC_df.rds") +load(file="../../../../data/Pheno_pla.Rdata") +load(file="../../../../data/geno_pheno_pla.Rdata") +load(file="../../../../data/pheno_df_pla.Rdata") +go_all_genes_number=readRDS(file="../../../../data/priors/go/go_all_genes_number.rds") +go_all_markers_number=readRDS(file="../../../../data/priors/go/go_all_markers_number.rds") +go_all_markers=readRDS(file="../../../../data/priors/go/go_all_markers.rds") +markerSets=readRDS(file="../../../../data/priors/go/markerSets.rds") +setsGF=readRDS(file="../../../../data/priors/go/setsGF.rds") +rsetsGF=readRDS(file="../../../../data/priors/go/rsetsGF.rds") +nsets=readRDS(file="../../../../data/priors/go/nsets.rds") +nsnps=readRDS(file="../../../../data/priors/go/nsnps.rds") +GF=readRDS(file="../../../../data/priors/go/GF.rds") +rGF=readRDS(file="../../../../data/priors/go/rGF.rds") ######################################################################################## #filter n=length(go_all_genes_number[go_all_markers_number>0]) @@ -63,7 +81,7 @@ rGF_filtered<-rGF_filtered[6001:7297] ########################################################################################### cycles=10; #gblup_validate=matrix(unlist(gblup_validate[[r]]),round(nrow(pheno_df_pla)/n_folds),byrow=TRUE); - gblup_validate=readRDS(file="/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/GBLUP/pla/8fold/gblup_validate_all.rds") + gblup_validate=readRDS(file="../../../GBLUP/pla/8fold/gblup_validate_all.rds") n_folds <- 8 T20_2_gblup_variances_all=rep(list(list()),cycles) diff --git a/code/using_GO/pla/gblup_vs_gfblup_using_go_analysis1.R b/code/using_GO/pla/gblup_vs_gfblup_using_go_analysis1.R index b950c2c9b784639a5280adb430e620a767cbfef9..a96dbbab94ca19cbb933bc1e8b14af082d21a1ee 100644 --- a/code/using_GO/pla/gblup_vs_gfblup_using_go_analysis1.R +++ b/code/using_GO/pla/gblup_vs_gfblup_using_go_analysis1.R @@ -2,7 +2,25 @@ ################################################################################################################################## # A N A L Y S I S ################################################################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/pla/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} +setwd(paste0(wdir,"/",wd,"/8fold/")); +################################################################################################################# + require(GO.db) T20_2_gblup_variances_all=readRDS(file="./T20_2_gblup_variances_all.rds") diff --git a/code/using_GO/psii/8fold/combine.R b/code/using_GO/psii/8fold/combine.R new file mode 100644 index 0000000000000000000000000000000000000000..374cd42ed98b127d8f4c9f9d95f8f9ef4027f7ea --- /dev/null +++ b/code/using_GO/psii/8fold/combine.R @@ -0,0 +1,1258 @@ +################################################################################################################################## +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} +setwd(paste0(wdir,"/",wd)); +################################################################################################################################## +L1_1_gblup_prediction_all_1_1000=readRDS(file="L1_1_gblup_prediction_all_1_1000.rds") +L1_1_gblup_prediction_all_1001_2000=readRDS(file="L1_1_gblup_prediction_all_1001_2000.rds") +L1_1_gblup_prediction_all_2001_3000=readRDS(file="L1_1_gblup_prediction_all_2001_3000.rds") +L1_1_gblup_prediction_all_3001_4000=readRDS(file="L1_1_gblup_prediction_all_3001_4000.rds") +L1_1_gblup_prediction_all_4001_5000=readRDS(file="L1_1_gblup_prediction_all_4001_5000.rds") +L1_1_gblup_prediction_all_5001_6000=readRDS(file="L1_1_gblup_prediction_all_5001_6000.rds") +L1_1_gblup_prediction_all_6001_7297=readRDS(file="L1_1_gblup_prediction_all_6001_7297.rds") +L1_1_gblup_prediction_all=c(L1_1_gblup_prediction_all_1_1000,L1_1_gblup_prediction_all_1001_2000,L1_1_gblup_prediction_all_2001_3000,L1_1_gblup_prediction_all_3001_4000,L1_1_gblup_prediction_all_4001_5000,L1_1_gblup_prediction_all_5001_6000,L1_1_gblup_prediction_all_6001_7297) + +L1_1_gblup_variances_all_1_1000=readRDS(file="L1_1_gblup_variances_all_1_1000.rds") +L1_1_gblup_variances_all_1001_2000=readRDS(file="L1_1_gblup_variances_all_1001_2000.rds") +L1_1_gblup_variances_all_2001_3000=readRDS(file="L1_1_gblup_variances_all_2001_3000.rds") +L1_1_gblup_variances_all_3001_4000=readRDS(file="L1_1_gblup_variances_all_3001_4000.rds") +L1_1_gblup_variances_all_4001_5000=readRDS(file="L1_1_gblup_variances_all_4001_5000.rds") +L1_1_gblup_variances_all_5001_6000=readRDS(file="L1_1_gblup_variances_all_5001_6000.rds") +L1_1_gblup_variances_all_6001_7297=readRDS(file="L1_1_gblup_variances_all_6001_7297.rds") +L1_1_gblup_variances_all=c(L1_1_gblup_variances_all_1_1000,L1_1_gblup_variances_all_1001_2000,L1_1_gblup_variances_all_2001_3000,L1_1_gblup_variances_all_3001_4000,L1_1_gblup_variances_all_4001_5000,L1_1_gblup_variances_all_5001_6000,L1_1_gblup_variances_all_6001_7297) + +saveRDS(L1_1_gblup_prediction_all,"L1_1_gblup_prediction_all.rds") +saveRDS(L1_1_gblup_variances_all,"L1_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +L1_1_gfblup_prediction_all_1_1000=readRDS(file="L1_1_gfblup_prediction_all_1_1000.rds") +L1_1_gfblup_prediction_all_1001_2000=readRDS(file="L1_1_gfblup_prediction_all_1001_2000.rds") +L1_1_gfblup_prediction_all_2001_3000=readRDS(file="L1_1_gfblup_prediction_all_2001_3000.rds") +L1_1_gfblup_prediction_all_3001_4000=readRDS(file="L1_1_gfblup_prediction_all_3001_4000.rds") +L1_1_gfblup_prediction_all_4001_5000=readRDS(file="L1_1_gfblup_prediction_all_4001_5000.rds") +L1_1_gfblup_prediction_all_5001_6000=readRDS(file="L1_1_gfblup_prediction_all_5001_6000.rds") +L1_1_gfblup_prediction_all_6001_7297=readRDS(file="L1_1_gfblup_prediction_all_6001_7297.rds") + +L1_1_gfblup_variances_all_1_1000=readRDS(file="L1_1_gfblup_variances_all_1_1000.rds") +L1_1_gfblup_variances_all_1001_2000=readRDS(file="L1_1_gfblup_variances_all_1001_2000.rds") +L1_1_gfblup_variances_all_2001_3000=readRDS(file="L1_1_gfblup_variances_all_2001_3000.rds") +L1_1_gfblup_variances_all_3001_4000=readRDS(file="L1_1_gfblup_variances_all_3001_4000.rds") +L1_1_gfblup_variances_all_4001_5000=readRDS(file="L1_1_gfblup_variances_all_4001_5000.rds") +L1_1_gfblup_variances_all_5001_6000=readRDS(file="L1_1_gfblup_variances_all_5001_6000.rds") +L1_1_gfblup_variances_all_6001_7297=readRDS(file="L1_1_gfblup_variances_all_6001_7297.rds") + +cycles=length(L1_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +L1_1_gfblup_variances_all=rep(list(list()),cycles) +L1_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_1_1000[[r]]) + L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_1001_2000[[r]]) + L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_2001_3000[[r]]) + L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_3001_4000[[r]]) + L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_4001_5000[[r]]) + L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_5001_6000[[r]]) + L1_1_gfblup_prediction_all[[r]]<-c(L1_1_gfblup_prediction_all[[r]],L1_1_gfblup_prediction_all_6001_7297[[r]]) + + L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_1_1000[[r]]) + L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_1001_2000[[r]]) + L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_2001_3000[[r]]) + L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_3001_4000[[r]]) + L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_4001_5000[[r]]) + L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_5001_6000[[r]]) + L1_1_gfblup_variances_all[[r]]<-c(L1_1_gfblup_variances_all[[r]],L1_1_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(L1_1_gfblup_prediction_all,"L1_1_gfblup_prediction_all.rds") +saveRDS(L1_1_gfblup_variances_all,"L1_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +L1_2_gblup_prediction_all_1_1000=readRDS(file="L1_2_gblup_prediction_all_1_1000.rds") +L1_2_gblup_prediction_all_1001_2000=readRDS(file="L1_2_gblup_prediction_all_1001_2000.rds") +L1_2_gblup_prediction_all_2001_3000=readRDS(file="L1_2_gblup_prediction_all_2001_3000.rds") +L1_2_gblup_prediction_all_3001_4000=readRDS(file="L1_2_gblup_prediction_all_3001_4000.rds") +L1_2_gblup_prediction_all_4001_5000=readRDS(file="L1_2_gblup_prediction_all_4001_5000.rds") +L1_2_gblup_prediction_all_5001_6000=readRDS(file="L1_2_gblup_prediction_all_5001_6000.rds") +L1_2_gblup_prediction_all_6001_7297=readRDS(file="L1_2_gblup_prediction_all_6001_7297.rds") +L1_2_gblup_prediction_all=c(L1_2_gblup_prediction_all_1_1000,L1_2_gblup_prediction_all_1001_2000,L1_2_gblup_prediction_all_2001_3000,L1_2_gblup_prediction_all_3001_4000,L1_2_gblup_prediction_all_4001_5000,L1_2_gblup_prediction_all_5001_6000,L1_2_gblup_prediction_all_6001_7297) + +L1_2_gblup_variances_all_1_1000=readRDS(file="L1_2_gblup_variances_all_1_1000.rds") +L1_2_gblup_variances_all_1001_2000=readRDS(file="L1_2_gblup_variances_all_1001_2000.rds") +L1_2_gblup_variances_all_2001_3000=readRDS(file="L1_2_gblup_variances_all_2001_3000.rds") +L1_2_gblup_variances_all_3001_4000=readRDS(file="L1_2_gblup_variances_all_3001_4000.rds") +L1_2_gblup_variances_all_4001_5000=readRDS(file="L1_2_gblup_variances_all_4001_5000.rds") +L1_2_gblup_variances_all_5001_6000=readRDS(file="L1_2_gblup_variances_all_5001_6000.rds") +L1_2_gblup_variances_all_6001_7297=readRDS(file="L1_2_gblup_variances_all_6001_7297.rds") +L1_2_gblup_variances_all=c(L1_2_gblup_variances_all_1_1000,L1_2_gblup_variances_all_1001_2000,L1_2_gblup_variances_all_2001_3000,L1_2_gblup_variances_all_3001_4000,L1_2_gblup_variances_all_4001_5000,L1_2_gblup_variances_all_5001_6000,L1_2_gblup_variances_all_6001_7297) + +saveRDS(L1_2_gblup_prediction_all,"L1_2_gblup_prediction_all.rds") +saveRDS(L1_2_gblup_variances_all,"L1_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +L1_2_gfblup_prediction_all_1_1000=readRDS(file="L1_2_gfblup_prediction_all_1_1000.rds") +L1_2_gfblup_prediction_all_1001_2000=readRDS(file="L1_2_gfblup_prediction_all_1001_2000.rds") +L1_2_gfblup_prediction_all_2001_3000=readRDS(file="L1_2_gfblup_prediction_all_2001_3000.rds") +L1_2_gfblup_prediction_all_3001_4000=readRDS(file="L1_2_gfblup_prediction_all_3001_4000.rds") +L1_2_gfblup_prediction_all_4001_5000=readRDS(file="L1_2_gfblup_prediction_all_4001_5000.rds") +L1_2_gfblup_prediction_all_5001_6000=readRDS(file="L1_2_gfblup_prediction_all_5001_6000.rds") +L1_2_gfblup_prediction_all_6001_7297=readRDS(file="L1_2_gfblup_prediction_all_6001_7297.rds") + +L1_2_gfblup_variances_all_1_1000=readRDS(file="L1_2_gfblup_variances_all_1_1000.rds") +L1_2_gfblup_variances_all_1001_2000=readRDS(file="L1_2_gfblup_variances_all_1001_2000.rds") +L1_2_gfblup_variances_all_2001_3000=readRDS(file="L1_2_gfblup_variances_all_2001_3000.rds") +L1_2_gfblup_variances_all_3001_4000=readRDS(file="L1_2_gfblup_variances_all_3001_4000.rds") +L1_2_gfblup_variances_all_4001_5000=readRDS(file="L1_2_gfblup_variances_all_4001_5000.rds") +L1_2_gfblup_variances_all_5001_6000=readRDS(file="L1_2_gfblup_variances_all_5001_6000.rds") +L1_2_gfblup_variances_all_6001_7297=readRDS(file="L1_2_gfblup_variances_all_6001_7297.rds") + +cycles=length(L1_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +L1_2_gfblup_variances_all=rep(list(list()),cycles) +L1_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_1_1000[[r]]) + L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_1001_2000[[r]]) + L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_2001_3000[[r]]) + L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_3001_4000[[r]]) + L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_4001_5000[[r]]) + L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_5001_6000[[r]]) + L1_2_gfblup_prediction_all[[r]]<-c(L1_2_gfblup_prediction_all[[r]],L1_2_gfblup_prediction_all_6001_7297[[r]]) + + L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_1_1000[[r]]) + L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_1001_2000[[r]]) + L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_2001_3000[[r]]) + L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_3001_4000[[r]]) + L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_4001_5000[[r]]) + L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_5001_6000[[r]]) + L1_2_gfblup_variances_all[[r]]<-c(L1_2_gfblup_variances_all[[r]],L1_2_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(L1_2_gfblup_prediction_all,"L1_2_gfblup_prediction_all.rds") +saveRDS(L1_2_gfblup_variances_all,"L1_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +L1_3_gblup_prediction_all_1_1000=readRDS(file="L1_3_gblup_prediction_all_1_1000.rds") +L1_3_gblup_prediction_all_1001_2000=readRDS(file="L1_3_gblup_prediction_all_1001_2000.rds") +L1_3_gblup_prediction_all_2001_3000=readRDS(file="L1_3_gblup_prediction_all_2001_3000.rds") +L1_3_gblup_prediction_all_3001_4000=readRDS(file="L1_3_gblup_prediction_all_3001_4000.rds") +L1_3_gblup_prediction_all_4001_5000=readRDS(file="L1_3_gblup_prediction_all_4001_5000.rds") +L1_3_gblup_prediction_all_5001_6000=readRDS(file="L1_3_gblup_prediction_all_5001_6000.rds") +L1_3_gblup_prediction_all_6001_7297=readRDS(file="L1_3_gblup_prediction_all_6001_7297.rds") +L1_3_gblup_prediction_all=c(L1_3_gblup_prediction_all_1_1000,L1_3_gblup_prediction_all_1001_2000,L1_3_gblup_prediction_all_2001_3000,L1_3_gblup_prediction_all_3001_4000,L1_3_gblup_prediction_all_4001_5000,L1_3_gblup_prediction_all_5001_6000,L1_3_gblup_prediction_all_6001_7297) + +L1_3_gblup_variances_all_1_1000=readRDS(file="L1_3_gblup_variances_all_1_1000.rds") +L1_3_gblup_variances_all_1001_2000=readRDS(file="L1_3_gblup_variances_all_1001_2000.rds") +L1_3_gblup_variances_all_2001_3000=readRDS(file="L1_3_gblup_variances_all_2001_3000.rds") +L1_3_gblup_variances_all_3001_4000=readRDS(file="L1_3_gblup_variances_all_3001_4000.rds") +L1_3_gblup_variances_all_4001_5000=readRDS(file="L1_3_gblup_variances_all_4001_5000.rds") +L1_3_gblup_variances_all_5001_6000=readRDS(file="L1_3_gblup_variances_all_5001_6000.rds") +L1_3_gblup_variances_all_6001_7297=readRDS(file="L1_3_gblup_variances_all_6001_7297.rds") +L1_3_gblup_variances_all=c(L1_3_gblup_variances_all_1_1000,L1_3_gblup_variances_all_1001_2000,L1_3_gblup_variances_all_2001_3000,L1_3_gblup_variances_all_3001_4000,L1_3_gblup_variances_all_4001_5000,L1_3_gblup_variances_all_5001_6000,L1_3_gblup_variances_all_6001_7297) + +saveRDS(L1_3_gblup_prediction_all,"L1_3_gblup_prediction_all.rds") +saveRDS(L1_3_gblup_variances_all,"L1_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +L1_3_gfblup_prediction_all_1_1000=readRDS(file="L1_3_gfblup_prediction_all_1_1000.rds") +L1_3_gfblup_prediction_all_1001_2000=readRDS(file="L1_3_gfblup_prediction_all_1001_2000.rds") +L1_3_gfblup_prediction_all_2001_3000=readRDS(file="L1_3_gfblup_prediction_all_2001_3000.rds") +L1_3_gfblup_prediction_all_3001_4000=readRDS(file="L1_3_gfblup_prediction_all_3001_4000.rds") +L1_3_gfblup_prediction_all_4001_5000=readRDS(file="L1_3_gfblup_prediction_all_4001_5000.rds") +L1_3_gfblup_prediction_all_5001_6000=readRDS(file="L1_3_gfblup_prediction_all_5001_6000.rds") +L1_3_gfblup_prediction_all_6001_7297=readRDS(file="L1_3_gfblup_prediction_all_6001_7297.rds") + +L1_3_gfblup_variances_all_1_1000=readRDS(file="L1_3_gfblup_variances_all_1_1000.rds") +L1_3_gfblup_variances_all_1001_2000=readRDS(file="L1_3_gfblup_variances_all_1001_2000.rds") +L1_3_gfblup_variances_all_2001_3000=readRDS(file="L1_3_gfblup_variances_all_2001_3000.rds") +L1_3_gfblup_variances_all_3001_4000=readRDS(file="L1_3_gfblup_variances_all_3001_4000.rds") +L1_3_gfblup_variances_all_4001_5000=readRDS(file="L1_3_gfblup_variances_all_4001_5000.rds") +L1_3_gfblup_variances_all_5001_6000=readRDS(file="L1_3_gfblup_variances_all_5001_6000.rds") +L1_3_gfblup_variances_all_6001_7297=readRDS(file="L1_3_gfblup_variances_all_6001_7297.rds") + +cycles=length(L1_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +L1_3_gfblup_variances_all=rep(list(list()),cycles) +L1_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_1_1000[[r]]) + L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_1001_2000[[r]]) + L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_2001_3000[[r]]) + L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_3001_4000[[r]]) + L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_4001_5000[[r]]) + L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_5001_6000[[r]]) + L1_3_gfblup_prediction_all[[r]]<-c(L1_3_gfblup_prediction_all[[r]],L1_3_gfblup_prediction_all_6001_7297[[r]]) + + L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_1_1000[[r]]) + L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_1001_2000[[r]]) + L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_2001_3000[[r]]) + L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_3001_4000[[r]]) + L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_4001_5000[[r]]) + L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_5001_6000[[r]]) + L1_3_gfblup_variances_all[[r]]<-c(L1_3_gfblup_variances_all[[r]],L1_3_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(L1_3_gfblup_prediction_all,"L1_3_gfblup_prediction_all.rds") +saveRDS(L1_3_gfblup_variances_all,"L1_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +L2_1_gblup_prediction_all_1_1000=readRDS(file="L2_1_gblup_prediction_all_1_1000.rds") +L2_1_gblup_prediction_all_1001_2000=readRDS(file="L2_1_gblup_prediction_all_1001_2000.rds") +L2_1_gblup_prediction_all_2001_3000=readRDS(file="L2_1_gblup_prediction_all_2001_3000.rds") +L2_1_gblup_prediction_all_3001_4000=readRDS(file="L2_1_gblup_prediction_all_3001_4000.rds") +L2_1_gblup_prediction_all_4001_5000=readRDS(file="L2_1_gblup_prediction_all_4001_5000.rds") +L2_1_gblup_prediction_all_5001_6000=readRDS(file="L2_1_gblup_prediction_all_5001_6000.rds") +L2_1_gblup_prediction_all_6001_7297=readRDS(file="L2_1_gblup_prediction_all_6001_7297.rds") +L2_1_gblup_prediction_all=c(L2_1_gblup_prediction_all_1_1000,L2_1_gblup_prediction_all_1001_2000,L2_1_gblup_prediction_all_2001_3000,L2_1_gblup_prediction_all_3001_4000,L2_1_gblup_prediction_all_4001_5000,L2_1_gblup_prediction_all_5001_6000,L2_1_gblup_prediction_all_6001_7297) + +L2_1_gblup_variances_all_1_1000=readRDS(file="L2_1_gblup_variances_all_1_1000.rds") +L2_1_gblup_variances_all_1001_2000=readRDS(file="L2_1_gblup_variances_all_1001_2000.rds") +L2_1_gblup_variances_all_2001_3000=readRDS(file="L2_1_gblup_variances_all_2001_3000.rds") +L2_1_gblup_variances_all_3001_4000=readRDS(file="L2_1_gblup_variances_all_3001_4000.rds") +L2_1_gblup_variances_all_4001_5000=readRDS(file="L2_1_gblup_variances_all_4001_5000.rds") +L2_1_gblup_variances_all_5001_6000=readRDS(file="L2_1_gblup_variances_all_5001_6000.rds") +L2_1_gblup_variances_all_6001_7297=readRDS(file="L2_1_gblup_variances_all_6001_7297.rds") +L2_1_gblup_variances_all=c(L2_1_gblup_variances_all_1_1000,L2_1_gblup_variances_all_1001_2000,L2_1_gblup_variances_all_2001_3000,L2_1_gblup_variances_all_3001_4000,L2_1_gblup_variances_all_4001_5000,L2_1_gblup_variances_all_5001_6000,L2_1_gblup_variances_all_6001_7297) + +saveRDS(L2_1_gblup_prediction_all,"L2_1_gblup_prediction_all.rds") +saveRDS(L2_1_gblup_variances_all,"L2_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +L2_1_gfblup_prediction_all_1_1000=readRDS(file="L2_1_gfblup_prediction_all_1_1000.rds") +L2_1_gfblup_prediction_all_1001_2000=readRDS(file="L2_1_gfblup_prediction_all_1001_2000.rds") +L2_1_gfblup_prediction_all_2001_3000=readRDS(file="L2_1_gfblup_prediction_all_2001_3000.rds") +L2_1_gfblup_prediction_all_3001_4000=readRDS(file="L2_1_gfblup_prediction_all_3001_4000.rds") +L2_1_gfblup_prediction_all_4001_5000=readRDS(file="L2_1_gfblup_prediction_all_4001_5000.rds") +L2_1_gfblup_prediction_all_5001_6000=readRDS(file="L2_1_gfblup_prediction_all_5001_6000.rds") +L2_1_gfblup_prediction_all_6001_7297=readRDS(file="L2_1_gfblup_prediction_all_6001_7297.rds") + +L2_1_gfblup_variances_all_1_1000=readRDS(file="L2_1_gfblup_variances_all_1_1000.rds") +L2_1_gfblup_variances_all_1001_2000=readRDS(file="L2_1_gfblup_variances_all_1001_2000.rds") +L2_1_gfblup_variances_all_2001_3000=readRDS(file="L2_1_gfblup_variances_all_2001_3000.rds") +L2_1_gfblup_variances_all_3001_4000=readRDS(file="L2_1_gfblup_variances_all_3001_4000.rds") +L2_1_gfblup_variances_all_4001_5000=readRDS(file="L2_1_gfblup_variances_all_4001_5000.rds") +L2_1_gfblup_variances_all_5001_6000=readRDS(file="L2_1_gfblup_variances_all_5001_6000.rds") +L2_1_gfblup_variances_all_6001_7297=readRDS(file="L2_1_gfblup_variances_all_6001_7297.rds") + +cycles=length(L2_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +L2_1_gfblup_variances_all=rep(list(list()),cycles) +L2_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_1_1000[[r]]) + L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_1001_2000[[r]]) + L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_2001_3000[[r]]) + L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_3001_4000[[r]]) + L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_4001_5000[[r]]) + L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_5001_6000[[r]]) + L2_1_gfblup_prediction_all[[r]]<-c(L2_1_gfblup_prediction_all[[r]],L2_1_gfblup_prediction_all_6001_7297[[r]]) + + L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_1_1000[[r]]) + L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_1001_2000[[r]]) + L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_2001_3000[[r]]) + L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_3001_4000[[r]]) + L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_4001_5000[[r]]) + L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_5001_6000[[r]]) + L2_1_gfblup_variances_all[[r]]<-c(L2_1_gfblup_variances_all[[r]],L2_1_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(L2_1_gfblup_prediction_all,"L2_1_gfblup_prediction_all.rds") +saveRDS(L2_1_gfblup_variances_all,"L2_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +L2_2_gblup_prediction_all_1_1000=readRDS(file="L2_2_gblup_prediction_all_1_1000.rds") +L2_2_gblup_prediction_all_1001_2000=readRDS(file="L2_2_gblup_prediction_all_1001_2000.rds") +L2_2_gblup_prediction_all_2001_3000=readRDS(file="L2_2_gblup_prediction_all_2001_3000.rds") +L2_2_gblup_prediction_all_3001_4000=readRDS(file="L2_2_gblup_prediction_all_3001_4000.rds") +L2_2_gblup_prediction_all_4001_5000=readRDS(file="L2_2_gblup_prediction_all_4001_5000.rds") +L2_2_gblup_prediction_all_5001_6000=readRDS(file="L2_2_gblup_prediction_all_5001_6000.rds") +L2_2_gblup_prediction_all_6001_7297=readRDS(file="L2_2_gblup_prediction_all_6001_7297.rds") +L2_2_gblup_prediction_all=c(L2_2_gblup_prediction_all_1_1000,L2_2_gblup_prediction_all_1001_2000,L2_2_gblup_prediction_all_2001_3000,L2_2_gblup_prediction_all_3001_4000,L2_2_gblup_prediction_all_4001_5000,L2_2_gblup_prediction_all_5001_6000,L2_2_gblup_prediction_all_6001_7297) + +L2_2_gblup_variances_all_1_1000=readRDS(file="L2_2_gblup_variances_all_1_1000.rds") +L2_2_gblup_variances_all_1001_2000=readRDS(file="L2_2_gblup_variances_all_1001_2000.rds") +L2_2_gblup_variances_all_2001_3000=readRDS(file="L2_2_gblup_variances_all_2001_3000.rds") +L2_2_gblup_variances_all_3001_4000=readRDS(file="L2_2_gblup_variances_all_3001_4000.rds") +L2_2_gblup_variances_all_4001_5000=readRDS(file="L2_2_gblup_variances_all_4001_5000.rds") +L2_2_gblup_variances_all_5001_6000=readRDS(file="L2_2_gblup_variances_all_5001_6000.rds") +L2_2_gblup_variances_all_6001_7297=readRDS(file="L2_2_gblup_variances_all_6001_7297.rds") +L2_2_gblup_variances_all=c(L2_2_gblup_variances_all_1_1000,L2_2_gblup_variances_all_1001_2000,L2_2_gblup_variances_all_2001_3000,L2_2_gblup_variances_all_3001_4000,L2_2_gblup_variances_all_4001_5000,L2_2_gblup_variances_all_5001_6000,L2_2_gblup_variances_all_6001_7297) + +saveRDS(L2_2_gblup_prediction_all,"L2_2_gblup_prediction_all.rds") +saveRDS(L2_2_gblup_variances_all,"L2_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +L2_2_gfblup_prediction_all_1_1000=readRDS(file="L2_2_gfblup_prediction_all_1_1000.rds") +L2_2_gfblup_prediction_all_1001_2000=readRDS(file="L2_2_gfblup_prediction_all_1001_2000.rds") +L2_2_gfblup_prediction_all_2001_3000=readRDS(file="L2_2_gfblup_prediction_all_2001_3000.rds") +L2_2_gfblup_prediction_all_3001_4000=readRDS(file="L2_2_gfblup_prediction_all_3001_4000.rds") +L2_2_gfblup_prediction_all_4001_5000=readRDS(file="L2_2_gfblup_prediction_all_4001_5000.rds") +L2_2_gfblup_prediction_all_5001_6000=readRDS(file="L2_2_gfblup_prediction_all_5001_6000.rds") +L2_2_gfblup_prediction_all_6001_7297=readRDS(file="L2_2_gfblup_prediction_all_6001_7297.rds") + +L2_2_gfblup_variances_all_1_1000=readRDS(file="L2_2_gfblup_variances_all_1_1000.rds") +L2_2_gfblup_variances_all_1001_2000=readRDS(file="L2_2_gfblup_variances_all_1001_2000.rds") +L2_2_gfblup_variances_all_2001_3000=readRDS(file="L2_2_gfblup_variances_all_2001_3000.rds") +L2_2_gfblup_variances_all_3001_4000=readRDS(file="L2_2_gfblup_variances_all_3001_4000.rds") +L2_2_gfblup_variances_all_4001_5000=readRDS(file="L2_2_gfblup_variances_all_4001_5000.rds") +L2_2_gfblup_variances_all_5001_6000=readRDS(file="L2_2_gfblup_variances_all_5001_6000.rds") +L2_2_gfblup_variances_all_6001_7297=readRDS(file="L2_2_gfblup_variances_all_6001_7297.rds") + +cycles=length(L2_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +L2_2_gfblup_variances_all=rep(list(list()),cycles) +L2_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_1_1000[[r]]) + L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_1001_2000[[r]]) + L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_2001_3000[[r]]) + L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_3001_4000[[r]]) + L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_4001_5000[[r]]) + L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_5001_6000[[r]]) + L2_2_gfblup_prediction_all[[r]]<-c(L2_2_gfblup_prediction_all[[r]],L2_2_gfblup_prediction_all_6001_7297[[r]]) + + L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_1_1000[[r]]) + L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_1001_2000[[r]]) + L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_2001_3000[[r]]) + L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_3001_4000[[r]]) + L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_4001_5000[[r]]) + L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_5001_6000[[r]]) + L2_2_gfblup_variances_all[[r]]<-c(L2_2_gfblup_variances_all[[r]],L2_2_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(L2_2_gfblup_prediction_all,"L2_2_gfblup_prediction_all.rds") +saveRDS(L2_2_gfblup_variances_all,"L2_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +L2_3_gblup_prediction_all_1_1000=readRDS(file="L2_3_gblup_prediction_all_1_1000.rds") +L2_3_gblup_prediction_all_1001_2000=readRDS(file="L2_3_gblup_prediction_all_1001_2000.rds") +L2_3_gblup_prediction_all_2001_3000=readRDS(file="L2_3_gblup_prediction_all_2001_3000.rds") +L2_3_gblup_prediction_all_3001_4000=readRDS(file="L2_3_gblup_prediction_all_3001_4000.rds") +L2_3_gblup_prediction_all_4001_5000=readRDS(file="L2_3_gblup_prediction_all_4001_5000.rds") +L2_3_gblup_prediction_all_5001_6000=readRDS(file="L2_3_gblup_prediction_all_5001_6000.rds") +L2_3_gblup_prediction_all_6001_7297=readRDS(file="L2_3_gblup_prediction_all_6001_7297.rds") +L2_3_gblup_prediction_all=c(L2_3_gblup_prediction_all_1_1000,L2_3_gblup_prediction_all_1001_2000,L2_3_gblup_prediction_all_2001_3000,L2_3_gblup_prediction_all_3001_4000,L2_3_gblup_prediction_all_4001_5000,L2_3_gblup_prediction_all_5001_6000,L2_3_gblup_prediction_all_6001_7297) + +L2_3_gblup_variances_all_1_1000=readRDS(file="L2_3_gblup_variances_all_1_1000.rds") +L2_3_gblup_variances_all_1001_2000=readRDS(file="L2_3_gblup_variances_all_1001_2000.rds") +L2_3_gblup_variances_all_2001_3000=readRDS(file="L2_3_gblup_variances_all_2001_3000.rds") +L2_3_gblup_variances_all_3001_4000=readRDS(file="L2_3_gblup_variances_all_3001_4000.rds") +L2_3_gblup_variances_all_4001_5000=readRDS(file="L2_3_gblup_variances_all_4001_5000.rds") +L2_3_gblup_variances_all_5001_6000=readRDS(file="L2_3_gblup_variances_all_5001_6000.rds") +L2_3_gblup_variances_all_6001_7297=readRDS(file="L2_3_gblup_variances_all_6001_7297.rds") +L2_3_gblup_variances_all=c(L2_3_gblup_variances_all_1_1000,L2_3_gblup_variances_all_1001_2000,L2_3_gblup_variances_all_2001_3000,L2_3_gblup_variances_all_3001_4000,L2_3_gblup_variances_all_4001_5000,L2_3_gblup_variances_all_5001_6000,L2_3_gblup_variances_all_6001_7297) + +saveRDS(L2_3_gblup_prediction_all,"L2_3_gblup_prediction_all.rds") +saveRDS(L2_3_gblup_variances_all,"L2_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +L2_3_gfblup_prediction_all_1_1000=readRDS(file="L2_3_gfblup_prediction_all_1_1000.rds") +L2_3_gfblup_prediction_all_1001_2000=readRDS(file="L2_3_gfblup_prediction_all_1001_2000.rds") +L2_3_gfblup_prediction_all_2001_3000=readRDS(file="L2_3_gfblup_prediction_all_2001_3000.rds") +L2_3_gfblup_prediction_all_3001_4000=readRDS(file="L2_3_gfblup_prediction_all_3001_4000.rds") +L2_3_gfblup_prediction_all_4001_5000=readRDS(file="L2_3_gfblup_prediction_all_4001_5000.rds") +L2_3_gfblup_prediction_all_5001_6000=readRDS(file="L2_3_gfblup_prediction_all_5001_6000.rds") +L2_3_gfblup_prediction_all_6001_7297=readRDS(file="L2_3_gfblup_prediction_all_6001_7297.rds") + +L2_3_gfblup_variances_all_1_1000=readRDS(file="L2_3_gfblup_variances_all_1_1000.rds") +L2_3_gfblup_variances_all_1001_2000=readRDS(file="L2_3_gfblup_variances_all_1001_2000.rds") +L2_3_gfblup_variances_all_2001_3000=readRDS(file="L2_3_gfblup_variances_all_2001_3000.rds") +L2_3_gfblup_variances_all_3001_4000=readRDS(file="L2_3_gfblup_variances_all_3001_4000.rds") +L2_3_gfblup_variances_all_4001_5000=readRDS(file="L2_3_gfblup_variances_all_4001_5000.rds") +L2_3_gfblup_variances_all_5001_6000=readRDS(file="L2_3_gfblup_variances_all_5001_6000.rds") +L2_3_gfblup_variances_all_6001_7297=readRDS(file="L2_3_gfblup_variances_all_6001_7297.rds") + +cycles=length(L2_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +L2_3_gfblup_variances_all=rep(list(list()),cycles) +L2_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_1_1000[[r]]) + L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_1001_2000[[r]]) + L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_2001_3000[[r]]) + L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_3001_4000[[r]]) + L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_4001_5000[[r]]) + L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_5001_6000[[r]]) + L2_3_gfblup_prediction_all[[r]]<-c(L2_3_gfblup_prediction_all[[r]],L2_3_gfblup_prediction_all_6001_7297[[r]]) + + L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_1_1000[[r]]) + L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_1001_2000[[r]]) + L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_2001_3000[[r]]) + L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_3001_4000[[r]]) + L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_4001_5000[[r]]) + L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_5001_6000[[r]]) + L2_3_gfblup_variances_all[[r]]<-c(L2_3_gfblup_variances_all[[r]],L2_3_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(L2_3_gfblup_prediction_all,"L2_3_gfblup_prediction_all.rds") +saveRDS(L2_3_gfblup_variances_all,"L2_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H1_1_gblup_prediction_all_1_1000=readRDS(file="H1_1_gblup_prediction_all_1_1000.rds") +H1_1_gblup_prediction_all_1001_2000=readRDS(file="H1_1_gblup_prediction_all_1001_2000.rds") +H1_1_gblup_prediction_all_2001_3000=readRDS(file="H1_1_gblup_prediction_all_2001_3000.rds") +H1_1_gblup_prediction_all_3001_4000=readRDS(file="H1_1_gblup_prediction_all_3001_4000.rds") +H1_1_gblup_prediction_all_4001_5000=readRDS(file="H1_1_gblup_prediction_all_4001_5000.rds") +H1_1_gblup_prediction_all_5001_6000=readRDS(file="H1_1_gblup_prediction_all_5001_6000.rds") +H1_1_gblup_prediction_all_6001_7297=readRDS(file="H1_1_gblup_prediction_all_6001_7297.rds") +H1_1_gblup_prediction_all=c(H1_1_gblup_prediction_all_1_1000,H1_1_gblup_prediction_all_1001_2000,H1_1_gblup_prediction_all_2001_3000,H1_1_gblup_prediction_all_3001_4000,H1_1_gblup_prediction_all_4001_5000,H1_1_gblup_prediction_all_5001_6000,H1_1_gblup_prediction_all_6001_7297) + +H1_1_gblup_variances_all_1_1000=readRDS(file="H1_1_gblup_variances_all_1_1000.rds") +H1_1_gblup_variances_all_1001_2000=readRDS(file="H1_1_gblup_variances_all_1001_2000.rds") +H1_1_gblup_variances_all_2001_3000=readRDS(file="H1_1_gblup_variances_all_2001_3000.rds") +H1_1_gblup_variances_all_3001_4000=readRDS(file="H1_1_gblup_variances_all_3001_4000.rds") +H1_1_gblup_variances_all_4001_5000=readRDS(file="H1_1_gblup_variances_all_4001_5000.rds") +H1_1_gblup_variances_all_5001_6000=readRDS(file="H1_1_gblup_variances_all_5001_6000.rds") +H1_1_gblup_variances_all_6001_7297=readRDS(file="H1_1_gblup_variances_all_6001_7297.rds") +H1_1_gblup_variances_all=c(H1_1_gblup_variances_all_1_1000,H1_1_gblup_variances_all_1001_2000,H1_1_gblup_variances_all_2001_3000,H1_1_gblup_variances_all_3001_4000,H1_1_gblup_variances_all_4001_5000,H1_1_gblup_variances_all_5001_6000,H1_1_gblup_variances_all_6001_7297) + +saveRDS(H1_1_gblup_prediction_all,"H1_1_gblup_prediction_all.rds") +saveRDS(H1_1_gblup_variances_all,"H1_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H1_1_gfblup_prediction_all_1_1000=readRDS(file="H1_1_gfblup_prediction_all_1_1000.rds") +H1_1_gfblup_prediction_all_1001_2000=readRDS(file="H1_1_gfblup_prediction_all_1001_2000.rds") +H1_1_gfblup_prediction_all_2001_3000=readRDS(file="H1_1_gfblup_prediction_all_2001_3000.rds") +H1_1_gfblup_prediction_all_3001_4000=readRDS(file="H1_1_gfblup_prediction_all_3001_4000.rds") +H1_1_gfblup_prediction_all_4001_5000=readRDS(file="H1_1_gfblup_prediction_all_4001_5000.rds") +H1_1_gfblup_prediction_all_5001_6000=readRDS(file="H1_1_gfblup_prediction_all_5001_6000.rds") +H1_1_gfblup_prediction_all_6001_7297=readRDS(file="H1_1_gfblup_prediction_all_6001_7297.rds") + +H1_1_gfblup_variances_all_1_1000=readRDS(file="H1_1_gfblup_variances_all_1_1000.rds") +H1_1_gfblup_variances_all_1001_2000=readRDS(file="H1_1_gfblup_variances_all_1001_2000.rds") +H1_1_gfblup_variances_all_2001_3000=readRDS(file="H1_1_gfblup_variances_all_2001_3000.rds") +H1_1_gfblup_variances_all_3001_4000=readRDS(file="H1_1_gfblup_variances_all_3001_4000.rds") +H1_1_gfblup_variances_all_4001_5000=readRDS(file="H1_1_gfblup_variances_all_4001_5000.rds") +H1_1_gfblup_variances_all_5001_6000=readRDS(file="H1_1_gfblup_variances_all_5001_6000.rds") +H1_1_gfblup_variances_all_6001_7297=readRDS(file="H1_1_gfblup_variances_all_6001_7297.rds") + +cycles=length(H1_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H1_1_gfblup_variances_all=rep(list(list()),cycles) +H1_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_1_1000[[r]]) + H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_1001_2000[[r]]) + H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_2001_3000[[r]]) + H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_3001_4000[[r]]) + H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_4001_5000[[r]]) + H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_5001_6000[[r]]) + H1_1_gfblup_prediction_all[[r]]<-c(H1_1_gfblup_prediction_all[[r]],H1_1_gfblup_prediction_all_6001_7297[[r]]) + + H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_1_1000[[r]]) + H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_1001_2000[[r]]) + H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_2001_3000[[r]]) + H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_3001_4000[[r]]) + H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_4001_5000[[r]]) + H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_5001_6000[[r]]) + H1_1_gfblup_variances_all[[r]]<-c(H1_1_gfblup_variances_all[[r]],H1_1_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(H1_1_gfblup_prediction_all,"H1_1_gfblup_prediction_all.rds") +saveRDS(H1_1_gfblup_variances_all,"H1_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +H1_2_gblup_prediction_all_1_1000=readRDS(file="H1_2_gblup_prediction_all_1_1000.rds") +H1_2_gblup_prediction_all_1001_2000=readRDS(file="H1_2_gblup_prediction_all_1001_2000.rds") +H1_2_gblup_prediction_all_2001_3000=readRDS(file="H1_2_gblup_prediction_all_2001_3000.rds") +H1_2_gblup_prediction_all_3001_4000=readRDS(file="H1_2_gblup_prediction_all_3001_4000.rds") +H1_2_gblup_prediction_all_4001_5000=readRDS(file="H1_2_gblup_prediction_all_4001_5000.rds") +H1_2_gblup_prediction_all_5001_6000=readRDS(file="H1_2_gblup_prediction_all_5001_6000.rds") +H1_2_gblup_prediction_all_6001_7297=readRDS(file="H1_2_gblup_prediction_all_6001_7297.rds") +H1_2_gblup_prediction_all=c(H1_2_gblup_prediction_all_1_1000,H1_2_gblup_prediction_all_1001_2000,H1_2_gblup_prediction_all_2001_3000,H1_2_gblup_prediction_all_3001_4000,H1_2_gblup_prediction_all_4001_5000,H1_2_gblup_prediction_all_5001_6000,H1_2_gblup_prediction_all_6001_7297) + +H1_2_gblup_variances_all_1_1000=readRDS(file="H1_2_gblup_variances_all_1_1000.rds") +H1_2_gblup_variances_all_1001_2000=readRDS(file="H1_2_gblup_variances_all_1001_2000.rds") +H1_2_gblup_variances_all_2001_3000=readRDS(file="H1_2_gblup_variances_all_2001_3000.rds") +H1_2_gblup_variances_all_3001_4000=readRDS(file="H1_2_gblup_variances_all_3001_4000.rds") +H1_2_gblup_variances_all_4001_5000=readRDS(file="H1_2_gblup_variances_all_4001_5000.rds") +H1_2_gblup_variances_all_5001_6000=readRDS(file="H1_2_gblup_variances_all_5001_6000.rds") +H1_2_gblup_variances_all_6001_7297=readRDS(file="H1_2_gblup_variances_all_6001_7297.rds") +H1_2_gblup_variances_all=c(H1_2_gblup_variances_all_1_1000,H1_2_gblup_variances_all_1001_2000,H1_2_gblup_variances_all_2001_3000,H1_2_gblup_variances_all_3001_4000,H1_2_gblup_variances_all_4001_5000,H1_2_gblup_variances_all_5001_6000,H1_2_gblup_variances_all_6001_7297) + +saveRDS(H1_2_gblup_prediction_all,"H1_2_gblup_prediction_all.rds") +saveRDS(H1_2_gblup_variances_all,"H1_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H1_2_gfblup_prediction_all_1_1000=readRDS(file="H1_2_gfblup_prediction_all_1_1000.rds") +H1_2_gfblup_prediction_all_1001_2000=readRDS(file="H1_2_gfblup_prediction_all_1001_2000.rds") +H1_2_gfblup_prediction_all_2001_3000=readRDS(file="H1_2_gfblup_prediction_all_2001_3000.rds") +H1_2_gfblup_prediction_all_3001_4000=readRDS(file="H1_2_gfblup_prediction_all_3001_4000.rds") +H1_2_gfblup_prediction_all_4001_5000=readRDS(file="H1_2_gfblup_prediction_all_4001_5000.rds") +H1_2_gfblup_prediction_all_5001_6000=readRDS(file="H1_2_gfblup_prediction_all_5001_6000.rds") +H1_2_gfblup_prediction_all_6001_7297=readRDS(file="H1_2_gfblup_prediction_all_6001_7297.rds") + +H1_2_gfblup_variances_all_1_1000=readRDS(file="H1_2_gfblup_variances_all_1_1000.rds") +H1_2_gfblup_variances_all_1001_2000=readRDS(file="H1_2_gfblup_variances_all_1001_2000.rds") +H1_2_gfblup_variances_all_2001_3000=readRDS(file="H1_2_gfblup_variances_all_2001_3000.rds") +H1_2_gfblup_variances_all_3001_4000=readRDS(file="H1_2_gfblup_variances_all_3001_4000.rds") +H1_2_gfblup_variances_all_4001_5000=readRDS(file="H1_2_gfblup_variances_all_4001_5000.rds") +H1_2_gfblup_variances_all_5001_6000=readRDS(file="H1_2_gfblup_variances_all_5001_6000.rds") +H1_2_gfblup_variances_all_6001_7297=readRDS(file="H1_2_gfblup_variances_all_6001_7297.rds") + +cycles=length(H1_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H1_2_gfblup_variances_all=rep(list(list()),cycles) +H1_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_1_1000[[r]]) + H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_1001_2000[[r]]) + H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_2001_3000[[r]]) + H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_3001_4000[[r]]) + H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_4001_5000[[r]]) + H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_5001_6000[[r]]) + H1_2_gfblup_prediction_all[[r]]<-c(H1_2_gfblup_prediction_all[[r]],H1_2_gfblup_prediction_all_6001_7297[[r]]) + + H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_1_1000[[r]]) + H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_1001_2000[[r]]) + H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_2001_3000[[r]]) + H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_3001_4000[[r]]) + H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_4001_5000[[r]]) + H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_5001_6000[[r]]) + H1_2_gfblup_variances_all[[r]]<-c(H1_2_gfblup_variances_all[[r]],H1_2_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(H1_2_gfblup_prediction_all,"H1_2_gfblup_prediction_all.rds") +saveRDS(H1_2_gfblup_variances_all,"H1_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +H1_3_gblup_prediction_all_1_1000=readRDS(file="H1_3_gblup_prediction_all_1_1000.rds") +H1_3_gblup_prediction_all_1001_2000=readRDS(file="H1_3_gblup_prediction_all_1001_2000.rds") +H1_3_gblup_prediction_all_2001_3000=readRDS(file="H1_3_gblup_prediction_all_2001_3000.rds") +H1_3_gblup_prediction_all_3001_4000=readRDS(file="H1_3_gblup_prediction_all_3001_4000.rds") +H1_3_gblup_prediction_all_4001_5000=readRDS(file="H1_3_gblup_prediction_all_4001_5000.rds") +H1_3_gblup_prediction_all_5001_6000=readRDS(file="H1_3_gblup_prediction_all_5001_6000.rds") +H1_3_gblup_prediction_all_6001_7297=readRDS(file="H1_3_gblup_prediction_all_6001_7297.rds") +H1_3_gblup_prediction_all=c(H1_3_gblup_prediction_all_1_1000,H1_3_gblup_prediction_all_1001_2000,H1_3_gblup_prediction_all_2001_3000,H1_3_gblup_prediction_all_3001_4000,H1_3_gblup_prediction_all_4001_5000,H1_3_gblup_prediction_all_5001_6000,H1_3_gblup_prediction_all_6001_7297) + +H1_3_gblup_variances_all_1_1000=readRDS(file="H1_3_gblup_variances_all_1_1000.rds") +H1_3_gblup_variances_all_1001_2000=readRDS(file="H1_3_gblup_variances_all_1001_2000.rds") +H1_3_gblup_variances_all_2001_3000=readRDS(file="H1_3_gblup_variances_all_2001_3000.rds") +H1_3_gblup_variances_all_3001_4000=readRDS(file="H1_3_gblup_variances_all_3001_4000.rds") +H1_3_gblup_variances_all_4001_5000=readRDS(file="H1_3_gblup_variances_all_4001_5000.rds") +H1_3_gblup_variances_all_5001_6000=readRDS(file="H1_3_gblup_variances_all_5001_6000.rds") +H1_3_gblup_variances_all_6001_7297=readRDS(file="H1_3_gblup_variances_all_6001_7297.rds") +H1_3_gblup_variances_all=c(H1_3_gblup_variances_all_1_1000,H1_3_gblup_variances_all_1001_2000,H1_3_gblup_variances_all_2001_3000,H1_3_gblup_variances_all_3001_4000,H1_3_gblup_variances_all_4001_5000,H1_3_gblup_variances_all_5001_6000,H1_3_gblup_variances_all_6001_7297) + +saveRDS(H1_3_gblup_prediction_all,"H1_3_gblup_prediction_all.rds") +saveRDS(H1_3_gblup_variances_all,"H1_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H1_3_gfblup_prediction_all_1_1000=readRDS(file="H1_3_gfblup_prediction_all_1_1000.rds") +H1_3_gfblup_prediction_all_1001_2000=readRDS(file="H1_3_gfblup_prediction_all_1001_2000.rds") +H1_3_gfblup_prediction_all_2001_3000=readRDS(file="H1_3_gfblup_prediction_all_2001_3000.rds") +H1_3_gfblup_prediction_all_3001_4000=readRDS(file="H1_3_gfblup_prediction_all_3001_4000.rds") +H1_3_gfblup_prediction_all_4001_5000=readRDS(file="H1_3_gfblup_prediction_all_4001_5000.rds") +H1_3_gfblup_prediction_all_5001_6000=readRDS(file="H1_3_gfblup_prediction_all_5001_6000.rds") +H1_3_gfblup_prediction_all_6001_7297=readRDS(file="H1_3_gfblup_prediction_all_6001_7297.rds") + +H1_3_gfblup_variances_all_1_1000=readRDS(file="H1_3_gfblup_variances_all_1_1000.rds") +H1_3_gfblup_variances_all_1001_2000=readRDS(file="H1_3_gfblup_variances_all_1001_2000.rds") +H1_3_gfblup_variances_all_2001_3000=readRDS(file="H1_3_gfblup_variances_all_2001_3000.rds") +H1_3_gfblup_variances_all_3001_4000=readRDS(file="H1_3_gfblup_variances_all_3001_4000.rds") +H1_3_gfblup_variances_all_4001_5000=readRDS(file="H1_3_gfblup_variances_all_4001_5000.rds") +H1_3_gfblup_variances_all_5001_6000=readRDS(file="H1_3_gfblup_variances_all_5001_6000.rds") +H1_3_gfblup_variances_all_6001_7297=readRDS(file="H1_3_gfblup_variances_all_6001_7297.rds") + +cycles=length(H1_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H1_3_gfblup_variances_all=rep(list(list()),cycles) +H1_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_1_1000[[r]]) + H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_1001_2000[[r]]) + H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_2001_3000[[r]]) + H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_3001_4000[[r]]) + H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_4001_5000[[r]]) + H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_5001_6000[[r]]) + H1_3_gfblup_prediction_all[[r]]<-c(H1_3_gfblup_prediction_all[[r]],H1_3_gfblup_prediction_all_6001_7297[[r]]) + + H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_1_1000[[r]]) + H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_1001_2000[[r]]) + H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_2001_3000[[r]]) + H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_3001_4000[[r]]) + H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_4001_5000[[r]]) + H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_5001_6000[[r]]) + H1_3_gfblup_variances_all[[r]]<-c(H1_3_gfblup_variances_all[[r]],H1_3_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(H1_3_gfblup_prediction_all,"H1_3_gfblup_prediction_all.rds") +saveRDS(H1_3_gfblup_variances_all,"H1_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +H2_1_gblup_prediction_all_1_1000=readRDS(file="H2_1_gblup_prediction_all_1_1000.rds") +H2_1_gblup_prediction_all_1001_2000=readRDS(file="H2_1_gblup_prediction_all_1001_2000.rds") +H2_1_gblup_prediction_all_2001_3000=readRDS(file="H2_1_gblup_prediction_all_2001_3000.rds") +H2_1_gblup_prediction_all_3001_4000=readRDS(file="H2_1_gblup_prediction_all_3001_4000.rds") +H2_1_gblup_prediction_all_4001_5000=readRDS(file="H2_1_gblup_prediction_all_4001_5000.rds") +H2_1_gblup_prediction_all_5001_6000=readRDS(file="H2_1_gblup_prediction_all_5001_6000.rds") +H2_1_gblup_prediction_all_6001_7297=readRDS(file="H2_1_gblup_prediction_all_6001_7297.rds") +H2_1_gblup_prediction_all=c(H2_1_gblup_prediction_all_1_1000,H2_1_gblup_prediction_all_1001_2000,H2_1_gblup_prediction_all_2001_3000,H2_1_gblup_prediction_all_3001_4000,H2_1_gblup_prediction_all_4001_5000,H2_1_gblup_prediction_all_5001_6000,H2_1_gblup_prediction_all_6001_7297) + +H2_1_gblup_variances_all_1_1000=readRDS(file="H2_1_gblup_variances_all_1_1000.rds") +H2_1_gblup_variances_all_1001_2000=readRDS(file="H2_1_gblup_variances_all_1001_2000.rds") +H2_1_gblup_variances_all_2001_3000=readRDS(file="H2_1_gblup_variances_all_2001_3000.rds") +H2_1_gblup_variances_all_3001_4000=readRDS(file="H2_1_gblup_variances_all_3001_4000.rds") +H2_1_gblup_variances_all_4001_5000=readRDS(file="H2_1_gblup_variances_all_4001_5000.rds") +H2_1_gblup_variances_all_5001_6000=readRDS(file="H2_1_gblup_variances_all_5001_6000.rds") +H2_1_gblup_variances_all_6001_7297=readRDS(file="H2_1_gblup_variances_all_6001_7297.rds") +H2_1_gblup_variances_all=c(H2_1_gblup_variances_all_1_1000,H2_1_gblup_variances_all_1001_2000,H2_1_gblup_variances_all_2001_3000,H2_1_gblup_variances_all_3001_4000,H2_1_gblup_variances_all_4001_5000,H2_1_gblup_variances_all_5001_6000,H2_1_gblup_variances_all_6001_7297) + +saveRDS(H2_1_gblup_prediction_all,"H2_1_gblup_prediction_all.rds") +saveRDS(H2_1_gblup_variances_all,"H2_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H2_1_gfblup_prediction_all_1_1000=readRDS(file="H2_1_gfblup_prediction_all_1_1000.rds") +H2_1_gfblup_prediction_all_1001_2000=readRDS(file="H2_1_gfblup_prediction_all_1001_2000.rds") +H2_1_gfblup_prediction_all_2001_3000=readRDS(file="H2_1_gfblup_prediction_all_2001_3000.rds") +H2_1_gfblup_prediction_all_3001_4000=readRDS(file="H2_1_gfblup_prediction_all_3001_4000.rds") +H2_1_gfblup_prediction_all_4001_5000=readRDS(file="H2_1_gfblup_prediction_all_4001_5000.rds") +H2_1_gfblup_prediction_all_5001_6000=readRDS(file="H2_1_gfblup_prediction_all_5001_6000.rds") +H2_1_gfblup_prediction_all_6001_7297=readRDS(file="H2_1_gfblup_prediction_all_6001_7297.rds") + +H2_1_gfblup_variances_all_1_1000=readRDS(file="H2_1_gfblup_variances_all_1_1000.rds") +H2_1_gfblup_variances_all_1001_2000=readRDS(file="H2_1_gfblup_variances_all_1001_2000.rds") +H2_1_gfblup_variances_all_2001_3000=readRDS(file="H2_1_gfblup_variances_all_2001_3000.rds") +H2_1_gfblup_variances_all_3001_4000=readRDS(file="H2_1_gfblup_variances_all_3001_4000.rds") +H2_1_gfblup_variances_all_4001_5000=readRDS(file="H2_1_gfblup_variances_all_4001_5000.rds") +H2_1_gfblup_variances_all_5001_6000=readRDS(file="H2_1_gfblup_variances_all_5001_6000.rds") +H2_1_gfblup_variances_all_6001_7297=readRDS(file="H2_1_gfblup_variances_all_6001_7297.rds") + +cycles=length(H2_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H2_1_gfblup_variances_all=rep(list(list()),cycles) +H2_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_1_1000[[r]]) + H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_1001_2000[[r]]) + H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_2001_3000[[r]]) + H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_3001_4000[[r]]) + H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_4001_5000[[r]]) + H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_5001_6000[[r]]) + H2_1_gfblup_prediction_all[[r]]<-c(H2_1_gfblup_prediction_all[[r]],H2_1_gfblup_prediction_all_6001_7297[[r]]) + + H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_1_1000[[r]]) + H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_1001_2000[[r]]) + H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_2001_3000[[r]]) + H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_3001_4000[[r]]) + H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_4001_5000[[r]]) + H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_5001_6000[[r]]) + H2_1_gfblup_variances_all[[r]]<-c(H2_1_gfblup_variances_all[[r]],H2_1_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(H2_1_gfblup_prediction_all,"H2_1_gfblup_prediction_all.rds") +saveRDS(H2_1_gfblup_variances_all,"H2_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +H2_2_gblup_prediction_all_1_1000=readRDS(file="H2_2_gblup_prediction_all_1_1000.rds") +H2_2_gblup_prediction_all_1001_2000=readRDS(file="H2_2_gblup_prediction_all_1001_2000.rds") +H2_2_gblup_prediction_all_2001_3000=readRDS(file="H2_2_gblup_prediction_all_2001_3000.rds") +H2_2_gblup_prediction_all_3001_4000=readRDS(file="H2_2_gblup_prediction_all_3001_4000.rds") +H2_2_gblup_prediction_all_4001_5000=readRDS(file="H2_2_gblup_prediction_all_4001_5000.rds") +H2_2_gblup_prediction_all_5001_6000=readRDS(file="H2_2_gblup_prediction_all_5001_6000.rds") +H2_2_gblup_prediction_all_6001_7297=readRDS(file="H2_2_gblup_prediction_all_6001_7297.rds") +H2_2_gblup_prediction_all=c(H2_2_gblup_prediction_all_1_1000,H2_2_gblup_prediction_all_1001_2000,H2_2_gblup_prediction_all_2001_3000,H2_2_gblup_prediction_all_3001_4000,H2_2_gblup_prediction_all_4001_5000,H2_2_gblup_prediction_all_5001_6000,H2_2_gblup_prediction_all_6001_7297) + +H2_2_gblup_variances_all_1_1000=readRDS(file="H2_2_gblup_variances_all_1_1000.rds") +H2_2_gblup_variances_all_1001_2000=readRDS(file="H2_2_gblup_variances_all_1001_2000.rds") +H2_2_gblup_variances_all_2001_3000=readRDS(file="H2_2_gblup_variances_all_2001_3000.rds") +H2_2_gblup_variances_all_3001_4000=readRDS(file="H2_2_gblup_variances_all_3001_4000.rds") +H2_2_gblup_variances_all_4001_5000=readRDS(file="H2_2_gblup_variances_all_4001_5000.rds") +H2_2_gblup_variances_all_5001_6000=readRDS(file="H2_2_gblup_variances_all_5001_6000.rds") +H2_2_gblup_variances_all_6001_7297=readRDS(file="H2_2_gblup_variances_all_6001_7297.rds") +H2_2_gblup_variances_all=c(H2_2_gblup_variances_all_1_1000,H2_2_gblup_variances_all_1001_2000,H2_2_gblup_variances_all_2001_3000,H2_2_gblup_variances_all_3001_4000,H2_2_gblup_variances_all_4001_5000,H2_2_gblup_variances_all_5001_6000,H2_2_gblup_variances_all_6001_7297) + +saveRDS(H2_2_gblup_prediction_all,"H2_2_gblup_prediction_all.rds") +saveRDS(H2_2_gblup_variances_all,"H2_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H2_2_gfblup_prediction_all_1_1000=readRDS(file="H2_2_gfblup_prediction_all_1_1000.rds") +H2_2_gfblup_prediction_all_1001_2000=readRDS(file="H2_2_gfblup_prediction_all_1001_2000.rds") +H2_2_gfblup_prediction_all_2001_3000=readRDS(file="H2_2_gfblup_prediction_all_2001_3000.rds") +H2_2_gfblup_prediction_all_3001_4000=readRDS(file="H2_2_gfblup_prediction_all_3001_4000.rds") +H2_2_gfblup_prediction_all_4001_5000=readRDS(file="H2_2_gfblup_prediction_all_4001_5000.rds") +H2_2_gfblup_prediction_all_5001_6000=readRDS(file="H2_2_gfblup_prediction_all_5001_6000.rds") +H2_2_gfblup_prediction_all_6001_7297=readRDS(file="H2_2_gfblup_prediction_all_6001_7297.rds") + +H2_2_gfblup_variances_all_1_1000=readRDS(file="H2_2_gfblup_variances_all_1_1000.rds") +H2_2_gfblup_variances_all_1001_2000=readRDS(file="H2_2_gfblup_variances_all_1001_2000.rds") +H2_2_gfblup_variances_all_2001_3000=readRDS(file="H2_2_gfblup_variances_all_2001_3000.rds") +H2_2_gfblup_variances_all_3001_4000=readRDS(file="H2_2_gfblup_variances_all_3001_4000.rds") +H2_2_gfblup_variances_all_4001_5000=readRDS(file="H2_2_gfblup_variances_all_4001_5000.rds") +H2_2_gfblup_variances_all_5001_6000=readRDS(file="H2_2_gfblup_variances_all_5001_6000.rds") +H2_2_gfblup_variances_all_6001_7297=readRDS(file="H2_2_gfblup_variances_all_6001_7297.rds") + +cycles=length(H2_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H2_2_gfblup_variances_all=rep(list(list()),cycles) +H2_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_1_1000[[r]]) + H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_1001_2000[[r]]) + H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_2001_3000[[r]]) + H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_3001_4000[[r]]) + H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_4001_5000[[r]]) + H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_5001_6000[[r]]) + H2_2_gfblup_prediction_all[[r]]<-c(H2_2_gfblup_prediction_all[[r]],H2_2_gfblup_prediction_all_6001_7297[[r]]) + + H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_1_1000[[r]]) + H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_1001_2000[[r]]) + H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_2001_3000[[r]]) + H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_3001_4000[[r]]) + H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_4001_5000[[r]]) + H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_5001_6000[[r]]) + H2_2_gfblup_variances_all[[r]]<-c(H2_2_gfblup_variances_all[[r]],H2_2_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(H2_2_gfblup_prediction_all,"H2_2_gfblup_prediction_all.rds") +saveRDS(H2_2_gfblup_variances_all,"H2_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +H2_3_gblup_prediction_all_1_1000=readRDS(file="H2_3_gblup_prediction_all_1_1000.rds") +H2_3_gblup_prediction_all_1001_2000=readRDS(file="H2_3_gblup_prediction_all_1001_2000.rds") +H2_3_gblup_prediction_all_2001_3000=readRDS(file="H2_3_gblup_prediction_all_2001_3000.rds") +H2_3_gblup_prediction_all_3001_4000=readRDS(file="H2_3_gblup_prediction_all_3001_4000.rds") +H2_3_gblup_prediction_all_4001_5000=readRDS(file="H2_3_gblup_prediction_all_4001_5000.rds") +H2_3_gblup_prediction_all_5001_6000=readRDS(file="H2_3_gblup_prediction_all_5001_6000.rds") +H2_3_gblup_prediction_all_6001_7297=readRDS(file="H2_3_gblup_prediction_all_6001_7297.rds") +H2_3_gblup_prediction_all=c(H2_3_gblup_prediction_all_1_1000,H2_3_gblup_prediction_all_1001_2000,H2_3_gblup_prediction_all_2001_3000,H2_3_gblup_prediction_all_3001_4000,H2_3_gblup_prediction_all_4001_5000,H2_3_gblup_prediction_all_5001_6000,H2_3_gblup_prediction_all_6001_7297) + +H2_3_gblup_variances_all_1_1000=readRDS(file="H2_3_gblup_variances_all_1_1000.rds") +H2_3_gblup_variances_all_1001_2000=readRDS(file="H2_3_gblup_variances_all_1001_2000.rds") +H2_3_gblup_variances_all_2001_3000=readRDS(file="H2_3_gblup_variances_all_2001_3000.rds") +H2_3_gblup_variances_all_3001_4000=readRDS(file="H2_3_gblup_variances_all_3001_4000.rds") +H2_3_gblup_variances_all_4001_5000=readRDS(file="H2_3_gblup_variances_all_4001_5000.rds") +H2_3_gblup_variances_all_5001_6000=readRDS(file="H2_3_gblup_variances_all_5001_6000.rds") +H2_3_gblup_variances_all_6001_7297=readRDS(file="H2_3_gblup_variances_all_6001_7297.rds") +H2_3_gblup_variances_all=c(H2_3_gblup_variances_all_1_1000,H2_3_gblup_variances_all_1001_2000,H2_3_gblup_variances_all_2001_3000,H2_3_gblup_variances_all_3001_4000,H2_3_gblup_variances_all_4001_5000,H2_3_gblup_variances_all_5001_6000,H2_3_gblup_variances_all_6001_7297) + +saveRDS(H2_3_gblup_prediction_all,"H2_3_gblup_prediction_all.rds") +saveRDS(H2_3_gblup_variances_all,"H2_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H2_3_gfblup_prediction_all_1_1000=readRDS(file="H2_3_gfblup_prediction_all_1_1000.rds") +H2_3_gfblup_prediction_all_1001_2000=readRDS(file="H2_3_gfblup_prediction_all_1001_2000.rds") +H2_3_gfblup_prediction_all_2001_3000=readRDS(file="H2_3_gfblup_prediction_all_2001_3000.rds") +H2_3_gfblup_prediction_all_3001_4000=readRDS(file="H2_3_gfblup_prediction_all_3001_4000.rds") +H2_3_gfblup_prediction_all_4001_5000=readRDS(file="H2_3_gfblup_prediction_all_4001_5000.rds") +H2_3_gfblup_prediction_all_5001_6000=readRDS(file="H2_3_gfblup_prediction_all_5001_6000.rds") +H2_3_gfblup_prediction_all_6001_7297=readRDS(file="H2_3_gfblup_prediction_all_6001_7297.rds") + +H2_3_gfblup_variances_all_1_1000=readRDS(file="H2_3_gfblup_variances_all_1_1000.rds") +H2_3_gfblup_variances_all_1001_2000=readRDS(file="H2_3_gfblup_variances_all_1001_2000.rds") +H2_3_gfblup_variances_all_2001_3000=readRDS(file="H2_3_gfblup_variances_all_2001_3000.rds") +H2_3_gfblup_variances_all_3001_4000=readRDS(file="H2_3_gfblup_variances_all_3001_4000.rds") +H2_3_gfblup_variances_all_4001_5000=readRDS(file="H2_3_gfblup_variances_all_4001_5000.rds") +H2_3_gfblup_variances_all_5001_6000=readRDS(file="H2_3_gfblup_variances_all_5001_6000.rds") +H2_3_gfblup_variances_all_6001_7297=readRDS(file="H2_3_gfblup_variances_all_6001_7297.rds") + +cycles=length(H2_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H2_3_gfblup_variances_all=rep(list(list()),cycles) +H2_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_1_1000[[r]]) + H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_1001_2000[[r]]) + H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_2001_3000[[r]]) + H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_3001_4000[[r]]) + H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_4001_5000[[r]]) + H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_5001_6000[[r]]) + H2_3_gfblup_prediction_all[[r]]<-c(H2_3_gfblup_prediction_all[[r]],H2_3_gfblup_prediction_all_6001_7297[[r]]) + + H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_1_1000[[r]]) + H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_1001_2000[[r]]) + H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_2001_3000[[r]]) + H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_3001_4000[[r]]) + H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_4001_5000[[r]]) + H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_5001_6000[[r]]) + H2_3_gfblup_variances_all[[r]]<-c(H2_3_gfblup_variances_all[[r]],H2_3_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(H2_3_gfblup_prediction_all,"H2_3_gfblup_prediction_all.rds") +saveRDS(H2_3_gfblup_variances_all,"H2_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H3_1_gblup_prediction_all_1_1000=readRDS(file="H3_1_gblup_prediction_all_1_1000.rds") +H3_1_gblup_prediction_all_1001_2000=readRDS(file="H3_1_gblup_prediction_all_1001_2000.rds") +H3_1_gblup_prediction_all_2001_3000=readRDS(file="H3_1_gblup_prediction_all_2001_3000.rds") +H3_1_gblup_prediction_all_3001_4000=readRDS(file="H3_1_gblup_prediction_all_3001_4000.rds") +H3_1_gblup_prediction_all_4001_5000=readRDS(file="H3_1_gblup_prediction_all_4001_5000.rds") +H3_1_gblup_prediction_all_5001_6000=readRDS(file="H3_1_gblup_prediction_all_5001_6000.rds") +H3_1_gblup_prediction_all_6001_7297=readRDS(file="H3_1_gblup_prediction_all_6001_7297.rds") +H3_1_gblup_prediction_all=c(H3_1_gblup_prediction_all_1_1000,H3_1_gblup_prediction_all_1001_2000,H3_1_gblup_prediction_all_2001_3000,H3_1_gblup_prediction_all_3001_4000,H3_1_gblup_prediction_all_4001_5000,H3_1_gblup_prediction_all_5001_6000,H3_1_gblup_prediction_all_6001_7297) + +H3_1_gblup_variances_all_1_1000=readRDS(file="H3_1_gblup_variances_all_1_1000.rds") +H3_1_gblup_variances_all_1001_2000=readRDS(file="H3_1_gblup_variances_all_1001_2000.rds") +H3_1_gblup_variances_all_2001_3000=readRDS(file="H3_1_gblup_variances_all_2001_3000.rds") +H3_1_gblup_variances_all_3001_4000=readRDS(file="H3_1_gblup_variances_all_3001_4000.rds") +H3_1_gblup_variances_all_4001_5000=readRDS(file="H3_1_gblup_variances_all_4001_5000.rds") +H3_1_gblup_variances_all_5001_6000=readRDS(file="H3_1_gblup_variances_all_5001_6000.rds") +H3_1_gblup_variances_all_6001_7297=readRDS(file="H3_1_gblup_variances_all_6001_7297.rds") +H3_1_gblup_variances_all=c(H3_1_gblup_variances_all_1_1000,H3_1_gblup_variances_all_1001_2000,H3_1_gblup_variances_all_2001_3000,H3_1_gblup_variances_all_3001_4000,H3_1_gblup_variances_all_4001_5000,H3_1_gblup_variances_all_5001_6000,H3_1_gblup_variances_all_6001_7297) + +saveRDS(H3_1_gblup_prediction_all,"H3_1_gblup_prediction_all.rds") +saveRDS(H3_1_gblup_variances_all,"H3_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H3_1_gfblup_prediction_all_1_1000=readRDS(file="H3_1_gfblup_prediction_all_1_1000.rds") +H3_1_gfblup_prediction_all_1001_2000=readRDS(file="H3_1_gfblup_prediction_all_1001_2000.rds") +H3_1_gfblup_prediction_all_2001_3000=readRDS(file="H3_1_gfblup_prediction_all_2001_3000.rds") +H3_1_gfblup_prediction_all_3001_4000=readRDS(file="H3_1_gfblup_prediction_all_3001_4000.rds") +H3_1_gfblup_prediction_all_4001_5000=readRDS(file="H3_1_gfblup_prediction_all_4001_5000.rds") +H3_1_gfblup_prediction_all_5001_6000=readRDS(file="H3_1_gfblup_prediction_all_5001_6000.rds") +H3_1_gfblup_prediction_all_6001_7297=readRDS(file="H3_1_gfblup_prediction_all_6001_7297.rds") + +H3_1_gfblup_variances_all_1_1000=readRDS(file="H3_1_gfblup_variances_all_1_1000.rds") +H3_1_gfblup_variances_all_1001_2000=readRDS(file="H3_1_gfblup_variances_all_1001_2000.rds") +H3_1_gfblup_variances_all_2001_3000=readRDS(file="H3_1_gfblup_variances_all_2001_3000.rds") +H3_1_gfblup_variances_all_3001_4000=readRDS(file="H3_1_gfblup_variances_all_3001_4000.rds") +H3_1_gfblup_variances_all_4001_5000=readRDS(file="H3_1_gfblup_variances_all_4001_5000.rds") +H3_1_gfblup_variances_all_5001_6000=readRDS(file="H3_1_gfblup_variances_all_5001_6000.rds") +H3_1_gfblup_variances_all_6001_7297=readRDS(file="H3_1_gfblup_variances_all_6001_7297.rds") + +cycles=length(H3_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H3_1_gfblup_variances_all=rep(list(list()),cycles) +H3_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_1_1000[[r]]) + H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_1001_2000[[r]]) + H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_2001_3000[[r]]) + H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_3001_4000[[r]]) + H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_4001_5000[[r]]) + H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_5001_6000[[r]]) + H3_1_gfblup_prediction_all[[r]]<-c(H3_1_gfblup_prediction_all[[r]],H3_1_gfblup_prediction_all_6001_7297[[r]]) + + H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_1_1000[[r]]) + H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_1001_2000[[r]]) + H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_2001_3000[[r]]) + H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_3001_4000[[r]]) + H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_4001_5000[[r]]) + H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_5001_6000[[r]]) + H3_1_gfblup_variances_all[[r]]<-c(H3_1_gfblup_variances_all[[r]],H3_1_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(H3_1_gfblup_prediction_all,"H3_1_gfblup_prediction_all.rds") +saveRDS(H3_1_gfblup_variances_all,"H3_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +H3_2_gblup_prediction_all_1_1000=readRDS(file="H3_2_gblup_prediction_all_1_1000.rds") +H3_2_gblup_prediction_all_1001_2000=readRDS(file="H3_2_gblup_prediction_all_1001_2000.rds") +H3_2_gblup_prediction_all_2001_3000=readRDS(file="H3_2_gblup_prediction_all_2001_3000.rds") +H3_2_gblup_prediction_all_3001_4000=readRDS(file="H3_2_gblup_prediction_all_3001_4000.rds") +H3_2_gblup_prediction_all_4001_5000=readRDS(file="H3_2_gblup_prediction_all_4001_5000.rds") +H3_2_gblup_prediction_all_5001_6000=readRDS(file="H3_2_gblup_prediction_all_5001_6000.rds") +H3_2_gblup_prediction_all_6001_7297=readRDS(file="H3_2_gblup_prediction_all_6001_7297.rds") +H3_2_gblup_prediction_all=c(H3_2_gblup_prediction_all_1_1000,H3_2_gblup_prediction_all_1001_2000,H3_2_gblup_prediction_all_2001_3000,H3_2_gblup_prediction_all_3001_4000,H3_2_gblup_prediction_all_4001_5000,H3_2_gblup_prediction_all_5001_6000,H3_2_gblup_prediction_all_6001_7297) + +H3_2_gblup_variances_all_1_1000=readRDS(file="H3_2_gblup_variances_all_1_1000.rds") +H3_2_gblup_variances_all_1001_2000=readRDS(file="H3_2_gblup_variances_all_1001_2000.rds") +H3_2_gblup_variances_all_2001_3000=readRDS(file="H3_2_gblup_variances_all_2001_3000.rds") +H3_2_gblup_variances_all_3001_4000=readRDS(file="H3_2_gblup_variances_all_3001_4000.rds") +H3_2_gblup_variances_all_4001_5000=readRDS(file="H3_2_gblup_variances_all_4001_5000.rds") +H3_2_gblup_variances_all_5001_6000=readRDS(file="H3_2_gblup_variances_all_5001_6000.rds") +H3_2_gblup_variances_all_6001_7297=readRDS(file="H3_2_gblup_variances_all_6001_7297.rds") +H3_2_gblup_variances_all=c(H3_2_gblup_variances_all_1_1000,H3_2_gblup_variances_all_1001_2000,H3_2_gblup_variances_all_2001_3000,H3_2_gblup_variances_all_3001_4000,H3_2_gblup_variances_all_4001_5000,H3_2_gblup_variances_all_5001_6000,H3_2_gblup_variances_all_6001_7297) + +saveRDS(H3_2_gblup_prediction_all,"H3_2_gblup_prediction_all.rds") +saveRDS(H3_2_gblup_variances_all,"H3_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H3_2_gfblup_prediction_all_1_1000=readRDS(file="H3_2_gfblup_prediction_all_1_1000.rds") +H3_2_gfblup_prediction_all_1001_2000=readRDS(file="H3_2_gfblup_prediction_all_1001_2000.rds") +H3_2_gfblup_prediction_all_2001_3000=readRDS(file="H3_2_gfblup_prediction_all_2001_3000.rds") +H3_2_gfblup_prediction_all_3001_4000=readRDS(file="H3_2_gfblup_prediction_all_3001_4000.rds") +H3_2_gfblup_prediction_all_4001_5000=readRDS(file="H3_2_gfblup_prediction_all_4001_5000.rds") +H3_2_gfblup_prediction_all_5001_6000=readRDS(file="H3_2_gfblup_prediction_all_5001_6000.rds") +H3_2_gfblup_prediction_all_6001_7297=readRDS(file="H3_2_gfblup_prediction_all_6001_7297.rds") + +H3_2_gfblup_variances_all_1_1000=readRDS(file="H3_2_gfblup_variances_all_1_1000.rds") +H3_2_gfblup_variances_all_1001_2000=readRDS(file="H3_2_gfblup_variances_all_1001_2000.rds") +H3_2_gfblup_variances_all_2001_3000=readRDS(file="H3_2_gfblup_variances_all_2001_3000.rds") +H3_2_gfblup_variances_all_3001_4000=readRDS(file="H3_2_gfblup_variances_all_3001_4000.rds") +H3_2_gfblup_variances_all_4001_5000=readRDS(file="H3_2_gfblup_variances_all_4001_5000.rds") +H3_2_gfblup_variances_all_5001_6000=readRDS(file="H3_2_gfblup_variances_all_5001_6000.rds") +H3_2_gfblup_variances_all_6001_7297=readRDS(file="H3_2_gfblup_variances_all_6001_7297.rds") + +cycles=length(H3_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H3_2_gfblup_variances_all=rep(list(list()),cycles) +H3_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_1_1000[[r]]) + H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_1001_2000[[r]]) + H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_2001_3000[[r]]) + H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_3001_4000[[r]]) + H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_4001_5000[[r]]) + H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_5001_6000[[r]]) + H3_2_gfblup_prediction_all[[r]]<-c(H3_2_gfblup_prediction_all[[r]],H3_2_gfblup_prediction_all_6001_7297[[r]]) + + H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_1_1000[[r]]) + H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_1001_2000[[r]]) + H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_2001_3000[[r]]) + H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_3001_4000[[r]]) + H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_4001_5000[[r]]) + H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_5001_6000[[r]]) + H3_2_gfblup_variances_all[[r]]<-c(H3_2_gfblup_variances_all[[r]],H3_2_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(H3_2_gfblup_prediction_all,"H3_2_gfblup_prediction_all.rds") +saveRDS(H3_2_gfblup_variances_all,"H3_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +H3_3_gblup_prediction_all_1_1000=readRDS(file="H3_3_gblup_prediction_all_1_1000.rds") +H3_3_gblup_prediction_all_1001_2000=readRDS(file="H3_3_gblup_prediction_all_1001_2000.rds") +H3_3_gblup_prediction_all_2001_3000=readRDS(file="H3_3_gblup_prediction_all_2001_3000.rds") +H3_3_gblup_prediction_all_3001_4000=readRDS(file="H3_3_gblup_prediction_all_3001_4000.rds") +H3_3_gblup_prediction_all_4001_5000=readRDS(file="H3_3_gblup_prediction_all_4001_5000.rds") +H3_3_gblup_prediction_all_5001_6000=readRDS(file="H3_3_gblup_prediction_all_5001_6000.rds") +H3_3_gblup_prediction_all_6001_7297=readRDS(file="H3_3_gblup_prediction_all_6001_7297.rds") +H3_3_gblup_prediction_all=c(H3_3_gblup_prediction_all_1_1000,H3_3_gblup_prediction_all_1001_2000,H3_3_gblup_prediction_all_2001_3000,H3_3_gblup_prediction_all_3001_4000,H3_3_gblup_prediction_all_4001_5000,H3_3_gblup_prediction_all_5001_6000,H3_3_gblup_prediction_all_6001_7297) + +H3_3_gblup_variances_all_1_1000=readRDS(file="H3_3_gblup_variances_all_1_1000.rds") +H3_3_gblup_variances_all_1001_2000=readRDS(file="H3_3_gblup_variances_all_1001_2000.rds") +H3_3_gblup_variances_all_2001_3000=readRDS(file="H3_3_gblup_variances_all_2001_3000.rds") +H3_3_gblup_variances_all_3001_4000=readRDS(file="H3_3_gblup_variances_all_3001_4000.rds") +H3_3_gblup_variances_all_4001_5000=readRDS(file="H3_3_gblup_variances_all_4001_5000.rds") +H3_3_gblup_variances_all_5001_6000=readRDS(file="H3_3_gblup_variances_all_5001_6000.rds") +H3_3_gblup_variances_all_6001_7297=readRDS(file="H3_3_gblup_variances_all_6001_7297.rds") +H3_3_gblup_variances_all=c(H3_3_gblup_variances_all_1_1000,H3_3_gblup_variances_all_1001_2000,H3_3_gblup_variances_all_2001_3000,H3_3_gblup_variances_all_3001_4000,H3_3_gblup_variances_all_4001_5000,H3_3_gblup_variances_all_5001_6000,H3_3_gblup_variances_all_6001_7297) + +saveRDS(H3_3_gblup_prediction_all,"H3_3_gblup_prediction_all.rds") +saveRDS(H3_3_gblup_variances_all,"H3_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H3_3_gfblup_prediction_all_1_1000=readRDS(file="H3_3_gfblup_prediction_all_1_1000.rds") +H3_3_gfblup_prediction_all_1001_2000=readRDS(file="H3_3_gfblup_prediction_all_1001_2000.rds") +H3_3_gfblup_prediction_all_2001_3000=readRDS(file="H3_3_gfblup_prediction_all_2001_3000.rds") +H3_3_gfblup_prediction_all_3001_4000=readRDS(file="H3_3_gfblup_prediction_all_3001_4000.rds") +H3_3_gfblup_prediction_all_4001_5000=readRDS(file="H3_3_gfblup_prediction_all_4001_5000.rds") +H3_3_gfblup_prediction_all_5001_6000=readRDS(file="H3_3_gfblup_prediction_all_5001_6000.rds") +H3_3_gfblup_prediction_all_6001_7297=readRDS(file="H3_3_gfblup_prediction_all_6001_7297.rds") + +H3_3_gfblup_variances_all_1_1000=readRDS(file="H3_3_gfblup_variances_all_1_1000.rds") +H3_3_gfblup_variances_all_1001_2000=readRDS(file="H3_3_gfblup_variances_all_1001_2000.rds") +H3_3_gfblup_variances_all_2001_3000=readRDS(file="H3_3_gfblup_variances_all_2001_3000.rds") +H3_3_gfblup_variances_all_3001_4000=readRDS(file="H3_3_gfblup_variances_all_3001_4000.rds") +H3_3_gfblup_variances_all_4001_5000=readRDS(file="H3_3_gfblup_variances_all_4001_5000.rds") +H3_3_gfblup_variances_all_5001_6000=readRDS(file="H3_3_gfblup_variances_all_5001_6000.rds") +H3_3_gfblup_variances_all_6001_7297=readRDS(file="H3_3_gfblup_variances_all_6001_7297.rds") + +cycles=length(H3_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H3_3_gfblup_variances_all=rep(list(list()),cycles) +H3_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_1_1000[[r]]) + H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_1001_2000[[r]]) + H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_2001_3000[[r]]) + H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_3001_4000[[r]]) + H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_4001_5000[[r]]) + H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_5001_6000[[r]]) + H3_3_gfblup_prediction_all[[r]]<-c(H3_3_gfblup_prediction_all[[r]],H3_3_gfblup_prediction_all_6001_7297[[r]]) + + H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_1_1000[[r]]) + H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_1001_2000[[r]]) + H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_2001_3000[[r]]) + H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_3001_4000[[r]]) + H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_4001_5000[[r]]) + H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_5001_6000[[r]]) + H3_3_gfblup_variances_all[[r]]<-c(H3_3_gfblup_variances_all[[r]],H3_3_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(H3_3_gfblup_prediction_all,"H3_3_gfblup_prediction_all.rds") +saveRDS(H3_3_gfblup_variances_all,"H3_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +H4_1_gblup_prediction_all_1_1000=readRDS(file="H4_1_gblup_prediction_all_1_1000.rds") +H4_1_gblup_prediction_all_1001_2000=readRDS(file="H4_1_gblup_prediction_all_1001_2000.rds") +H4_1_gblup_prediction_all_2001_3000=readRDS(file="H4_1_gblup_prediction_all_2001_3000.rds") +H4_1_gblup_prediction_all_3001_4000=readRDS(file="H4_1_gblup_prediction_all_3001_4000.rds") +H4_1_gblup_prediction_all_4001_5000=readRDS(file="H4_1_gblup_prediction_all_4001_5000.rds") +H4_1_gblup_prediction_all_5001_6000=readRDS(file="H4_1_gblup_prediction_all_5001_6000.rds") +H4_1_gblup_prediction_all_6001_7297=readRDS(file="H4_1_gblup_prediction_all_6001_7297.rds") +H4_1_gblup_prediction_all=c(H4_1_gblup_prediction_all_1_1000,H4_1_gblup_prediction_all_1001_2000,H4_1_gblup_prediction_all_2001_3000,H4_1_gblup_prediction_all_3001_4000,H4_1_gblup_prediction_all_4001_5000,H4_1_gblup_prediction_all_5001_6000,H4_1_gblup_prediction_all_6001_7297) + +H4_1_gblup_variances_all_1_1000=readRDS(file="H4_1_gblup_variances_all_1_1000.rds") +H4_1_gblup_variances_all_1001_2000=readRDS(file="H4_1_gblup_variances_all_1001_2000.rds") +H4_1_gblup_variances_all_2001_3000=readRDS(file="H4_1_gblup_variances_all_2001_3000.rds") +H4_1_gblup_variances_all_3001_4000=readRDS(file="H4_1_gblup_variances_all_3001_4000.rds") +H4_1_gblup_variances_all_4001_5000=readRDS(file="H4_1_gblup_variances_all_4001_5000.rds") +H4_1_gblup_variances_all_5001_6000=readRDS(file="H4_1_gblup_variances_all_5001_6000.rds") +H4_1_gblup_variances_all_6001_7297=readRDS(file="H4_1_gblup_variances_all_6001_7297.rds") +H4_1_gblup_variances_all=c(H4_1_gblup_variances_all_1_1000,H4_1_gblup_variances_all_1001_2000,H4_1_gblup_variances_all_2001_3000,H4_1_gblup_variances_all_3001_4000,H4_1_gblup_variances_all_4001_5000,H4_1_gblup_variances_all_5001_6000,H4_1_gblup_variances_all_6001_7297) + +saveRDS(H4_1_gblup_prediction_all,"H4_1_gblup_prediction_all.rds") +saveRDS(H4_1_gblup_variances_all,"H4_1_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H4_1_gfblup_prediction_all_1_1000=readRDS(file="H4_1_gfblup_prediction_all_1_1000.rds") +H4_1_gfblup_prediction_all_1001_2000=readRDS(file="H4_1_gfblup_prediction_all_1001_2000.rds") +H4_1_gfblup_prediction_all_2001_3000=readRDS(file="H4_1_gfblup_prediction_all_2001_3000.rds") +H4_1_gfblup_prediction_all_3001_4000=readRDS(file="H4_1_gfblup_prediction_all_3001_4000.rds") +H4_1_gfblup_prediction_all_4001_5000=readRDS(file="H4_1_gfblup_prediction_all_4001_5000.rds") +H4_1_gfblup_prediction_all_5001_6000=readRDS(file="H4_1_gfblup_prediction_all_5001_6000.rds") +H4_1_gfblup_prediction_all_6001_7297=readRDS(file="H4_1_gfblup_prediction_all_6001_7297.rds") + +H4_1_gfblup_variances_all_1_1000=readRDS(file="H4_1_gfblup_variances_all_1_1000.rds") +H4_1_gfblup_variances_all_1001_2000=readRDS(file="H4_1_gfblup_variances_all_1001_2000.rds") +H4_1_gfblup_variances_all_2001_3000=readRDS(file="H4_1_gfblup_variances_all_2001_3000.rds") +H4_1_gfblup_variances_all_3001_4000=readRDS(file="H4_1_gfblup_variances_all_3001_4000.rds") +H4_1_gfblup_variances_all_4001_5000=readRDS(file="H4_1_gfblup_variances_all_4001_5000.rds") +H4_1_gfblup_variances_all_5001_6000=readRDS(file="H4_1_gfblup_variances_all_5001_6000.rds") +H4_1_gfblup_variances_all_6001_7297=readRDS(file="H4_1_gfblup_variances_all_6001_7297.rds") + +cycles=length(H4_1_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H4_1_gfblup_variances_all=rep(list(list()),cycles) +H4_1_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_1_1000[[r]]) + H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_1001_2000[[r]]) + H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_2001_3000[[r]]) + H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_3001_4000[[r]]) + H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_4001_5000[[r]]) + H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_5001_6000[[r]]) + H4_1_gfblup_prediction_all[[r]]<-c(H4_1_gfblup_prediction_all[[r]],H4_1_gfblup_prediction_all_6001_7297[[r]]) + + H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_1_1000[[r]]) + H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_1001_2000[[r]]) + H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_2001_3000[[r]]) + H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_3001_4000[[r]]) + H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_4001_5000[[r]]) + H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_5001_6000[[r]]) + H4_1_gfblup_variances_all[[r]]<-c(H4_1_gfblup_variances_all[[r]],H4_1_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(H4_1_gfblup_prediction_all,"H4_1_gfblup_prediction_all.rds") +saveRDS(H4_1_gfblup_variances_all,"H4_1_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +H4_2_gblup_prediction_all_1_1000=readRDS(file="H4_2_gblup_prediction_all_1_1000.rds") +H4_2_gblup_prediction_all_1001_2000=readRDS(file="H4_2_gblup_prediction_all_1001_2000.rds") +H4_2_gblup_prediction_all_2001_3000=readRDS(file="H4_2_gblup_prediction_all_2001_3000.rds") +H4_2_gblup_prediction_all_3001_4000=readRDS(file="H4_2_gblup_prediction_all_3001_4000.rds") +H4_2_gblup_prediction_all_4001_5000=readRDS(file="H4_2_gblup_prediction_all_4001_5000.rds") +H4_2_gblup_prediction_all_5001_6000=readRDS(file="H4_2_gblup_prediction_all_5001_6000.rds") +H4_2_gblup_prediction_all_6001_7297=readRDS(file="H4_2_gblup_prediction_all_6001_7297.rds") +H4_2_gblup_prediction_all=c(H4_2_gblup_prediction_all_1_1000,H4_2_gblup_prediction_all_1001_2000,H4_2_gblup_prediction_all_2001_3000,H4_2_gblup_prediction_all_3001_4000,H4_2_gblup_prediction_all_4001_5000,H4_2_gblup_prediction_all_5001_6000,H4_2_gblup_prediction_all_6001_7297) + +H4_2_gblup_variances_all_1_1000=readRDS(file="H4_2_gblup_variances_all_1_1000.rds") +H4_2_gblup_variances_all_1001_2000=readRDS(file="H4_2_gblup_variances_all_1001_2000.rds") +H4_2_gblup_variances_all_2001_3000=readRDS(file="H4_2_gblup_variances_all_2001_3000.rds") +H4_2_gblup_variances_all_3001_4000=readRDS(file="H4_2_gblup_variances_all_3001_4000.rds") +H4_2_gblup_variances_all_4001_5000=readRDS(file="H4_2_gblup_variances_all_4001_5000.rds") +H4_2_gblup_variances_all_5001_6000=readRDS(file="H4_2_gblup_variances_all_5001_6000.rds") +H4_2_gblup_variances_all_6001_7297=readRDS(file="H4_2_gblup_variances_all_6001_7297.rds") +H4_2_gblup_variances_all=c(H4_2_gblup_variances_all_1_1000,H4_2_gblup_variances_all_1001_2000,H4_2_gblup_variances_all_2001_3000,H4_2_gblup_variances_all_3001_4000,H4_2_gblup_variances_all_4001_5000,H4_2_gblup_variances_all_5001_6000,H4_2_gblup_variances_all_6001_7297) + +saveRDS(H4_2_gblup_prediction_all,"H4_2_gblup_prediction_all.rds") +saveRDS(H4_2_gblup_variances_all,"H4_2_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H4_2_gfblup_prediction_all_1_1000=readRDS(file="H4_2_gfblup_prediction_all_1_1000.rds") +H4_2_gfblup_prediction_all_1001_2000=readRDS(file="H4_2_gfblup_prediction_all_1001_2000.rds") +H4_2_gfblup_prediction_all_2001_3000=readRDS(file="H4_2_gfblup_prediction_all_2001_3000.rds") +H4_2_gfblup_prediction_all_3001_4000=readRDS(file="H4_2_gfblup_prediction_all_3001_4000.rds") +H4_2_gfblup_prediction_all_4001_5000=readRDS(file="H4_2_gfblup_prediction_all_4001_5000.rds") +H4_2_gfblup_prediction_all_5001_6000=readRDS(file="H4_2_gfblup_prediction_all_5001_6000.rds") +H4_2_gfblup_prediction_all_6001_7297=readRDS(file="H4_2_gfblup_prediction_all_6001_7297.rds") + +H4_2_gfblup_variances_all_1_1000=readRDS(file="H4_2_gfblup_variances_all_1_1000.rds") +H4_2_gfblup_variances_all_1001_2000=readRDS(file="H4_2_gfblup_variances_all_1001_2000.rds") +H4_2_gfblup_variances_all_2001_3000=readRDS(file="H4_2_gfblup_variances_all_2001_3000.rds") +H4_2_gfblup_variances_all_3001_4000=readRDS(file="H4_2_gfblup_variances_all_3001_4000.rds") +H4_2_gfblup_variances_all_4001_5000=readRDS(file="H4_2_gfblup_variances_all_4001_5000.rds") +H4_2_gfblup_variances_all_5001_6000=readRDS(file="H4_2_gfblup_variances_all_5001_6000.rds") +H4_2_gfblup_variances_all_6001_7297=readRDS(file="H4_2_gfblup_variances_all_6001_7297.rds") + +cycles=length(H4_2_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H4_2_gfblup_variances_all=rep(list(list()),cycles) +H4_2_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_1_1000[[r]]) + H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_1001_2000[[r]]) + H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_2001_3000[[r]]) + H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_3001_4000[[r]]) + H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_4001_5000[[r]]) + H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_5001_6000[[r]]) + H4_2_gfblup_prediction_all[[r]]<-c(H4_2_gfblup_prediction_all[[r]],H4_2_gfblup_prediction_all_6001_7297[[r]]) + + H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_1_1000[[r]]) + H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_1001_2000[[r]]) + H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_2001_3000[[r]]) + H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_3001_4000[[r]]) + H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_4001_5000[[r]]) + H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_5001_6000[[r]]) + H4_2_gfblup_variances_all[[r]]<-c(H4_2_gfblup_variances_all[[r]],H4_2_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(H4_2_gfblup_prediction_all,"H4_2_gfblup_prediction_all.rds") +saveRDS(H4_2_gfblup_variances_all,"H4_2_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + +H4_3_gblup_prediction_all_1_1000=readRDS(file="H4_3_gblup_prediction_all_1_1000.rds") +H4_3_gblup_prediction_all_1001_2000=readRDS(file="H4_3_gblup_prediction_all_1001_2000.rds") +H4_3_gblup_prediction_all_2001_3000=readRDS(file="H4_3_gblup_prediction_all_2001_3000.rds") +H4_3_gblup_prediction_all_3001_4000=readRDS(file="H4_3_gblup_prediction_all_3001_4000.rds") +H4_3_gblup_prediction_all_4001_5000=readRDS(file="H4_3_gblup_prediction_all_4001_5000.rds") +H4_3_gblup_prediction_all_5001_6000=readRDS(file="H4_3_gblup_prediction_all_5001_6000.rds") +H4_3_gblup_prediction_all_6001_7297=readRDS(file="H4_3_gblup_prediction_all_6001_7297.rds") +H4_3_gblup_prediction_all=c(H4_3_gblup_prediction_all_1_1000,H4_3_gblup_prediction_all_1001_2000,H4_3_gblup_prediction_all_2001_3000,H4_3_gblup_prediction_all_3001_4000,H4_3_gblup_prediction_all_4001_5000,H4_3_gblup_prediction_all_5001_6000,H4_3_gblup_prediction_all_6001_7297) + +H4_3_gblup_variances_all_1_1000=readRDS(file="H4_3_gblup_variances_all_1_1000.rds") +H4_3_gblup_variances_all_1001_2000=readRDS(file="H4_3_gblup_variances_all_1001_2000.rds") +H4_3_gblup_variances_all_2001_3000=readRDS(file="H4_3_gblup_variances_all_2001_3000.rds") +H4_3_gblup_variances_all_3001_4000=readRDS(file="H4_3_gblup_variances_all_3001_4000.rds") +H4_3_gblup_variances_all_4001_5000=readRDS(file="H4_3_gblup_variances_all_4001_5000.rds") +H4_3_gblup_variances_all_5001_6000=readRDS(file="H4_3_gblup_variances_all_5001_6000.rds") +H4_3_gblup_variances_all_6001_7297=readRDS(file="H4_3_gblup_variances_all_6001_7297.rds") +H4_3_gblup_variances_all=c(H4_3_gblup_variances_all_1_1000,H4_3_gblup_variances_all_1001_2000,H4_3_gblup_variances_all_2001_3000,H4_3_gblup_variances_all_3001_4000,H4_3_gblup_variances_all_4001_5000,H4_3_gblup_variances_all_5001_6000,H4_3_gblup_variances_all_6001_7297) + +saveRDS(H4_3_gblup_prediction_all,"H4_3_gblup_prediction_all.rds") +saveRDS(H4_3_gblup_variances_all,"H4_3_gblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +H4_3_gfblup_prediction_all_1_1000=readRDS(file="H4_3_gfblup_prediction_all_1_1000.rds") +H4_3_gfblup_prediction_all_1001_2000=readRDS(file="H4_3_gfblup_prediction_all_1001_2000.rds") +H4_3_gfblup_prediction_all_2001_3000=readRDS(file="H4_3_gfblup_prediction_all_2001_3000.rds") +H4_3_gfblup_prediction_all_3001_4000=readRDS(file="H4_3_gfblup_prediction_all_3001_4000.rds") +H4_3_gfblup_prediction_all_4001_5000=readRDS(file="H4_3_gfblup_prediction_all_4001_5000.rds") +H4_3_gfblup_prediction_all_5001_6000=readRDS(file="H4_3_gfblup_prediction_all_5001_6000.rds") +H4_3_gfblup_prediction_all_6001_7297=readRDS(file="H4_3_gfblup_prediction_all_6001_7297.rds") + +H4_3_gfblup_variances_all_1_1000=readRDS(file="H4_3_gfblup_variances_all_1_1000.rds") +H4_3_gfblup_variances_all_1001_2000=readRDS(file="H4_3_gfblup_variances_all_1001_2000.rds") +H4_3_gfblup_variances_all_2001_3000=readRDS(file="H4_3_gfblup_variances_all_2001_3000.rds") +H4_3_gfblup_variances_all_3001_4000=readRDS(file="H4_3_gfblup_variances_all_3001_4000.rds") +H4_3_gfblup_variances_all_4001_5000=readRDS(file="H4_3_gfblup_variances_all_4001_5000.rds") +H4_3_gfblup_variances_all_5001_6000=readRDS(file="H4_3_gfblup_variances_all_5001_6000.rds") +H4_3_gfblup_variances_all_6001_7297=readRDS(file="H4_3_gfblup_variances_all_6001_7297.rds") + +cycles=length(H4_3_gfblup_prediction_all_1_1000) +n_folds <- 8 + +H4_3_gfblup_variances_all=rep(list(list()),cycles) +H4_3_gfblup_prediction_all=rep(list(list()),cycles) + +for(r in 1:cycles) +{ + H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_1_1000[[r]]) + H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_1001_2000[[r]]) + H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_2001_3000[[r]]) + H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_3001_4000[[r]]) + H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_4001_5000[[r]]) + H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_5001_6000[[r]]) + H4_3_gfblup_prediction_all[[r]]<-c(H4_3_gfblup_prediction_all[[r]],H4_3_gfblup_prediction_all_6001_7297[[r]]) + + H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_1_1000[[r]]) + H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_1001_2000[[r]]) + H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_2001_3000[[r]]) + H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_3001_4000[[r]]) + H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_4001_5000[[r]]) + H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_5001_6000[[r]]) + H4_3_gfblup_variances_all[[r]]<-c(H4_3_gfblup_variances_all[[r]],H4_3_gfblup_variances_all_6001_7297[[r]]) + +} + +saveRDS(H4_3_gfblup_prediction_all,"H4_3_gfblup_prediction_all.rds") +saveRDS(H4_3_gfblup_variances_all,"H4_3_gfblup_variances_all.rds") + +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ diff --git a/code/using_GO/psii/gblup_vs_gfblup_using_go_analysis1.R b/code/using_GO/psii/gblup_vs_gfblup_using_go_analysis1.R index e02a7325a37d1dab8162dc2a948f4f9d286a3abf..e0cc7505798140aad1322559c2c140dd5bf3acdf 100644 --- a/code/using_GO/psii/gblup_vs_gfblup_using_go_analysis1.R +++ b/code/using_GO/psii/gblup_vs_gfblup_using_go_analysis1.R @@ -2,7 +2,24 @@ ################################################################################################################################## # A N A L Y S I S ################################################################################################################################## -setwd("/mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/psii/8fold/") +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} +setwd(paste0(wdir,"/",wd,"/8fold/")); +################################################################################################################# require(GO.db) L2_2_gblup_variances_all=readRDS(file="./L2_2_gblup_variances_all.rds") @@ -110,42 +127,3 @@ saveRDS(L2_2_all,"L2_2_all_analysis1.rds") write.table(L2_2_all_important, file="L2_2_gblup_vs_gfblup_all_using_go_important_analysis1.tbl", sep = "\t", dec = ".",row.names = TRUE, col.names = TRUE) saveRDS(L2_2_all_important,"L2_2_all_important_analysis1.rds") #~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -################################################################################################################################## -# DIFFERENCE in RANDOM VS BIOLOGY DRIVEN SUBSET OF MARKERS (This doesn't seem to help alot, so no need to show this plot) -################################################################################################################################## -goid_important=rownames(L2_2_all_important) -go_all_markers_filtered_important=go_all_markers_filtered[names(go_all_markers_filtered) %in% goid_important] -gfb_pred_important=gfb_pred[names(gfb_pred) %in% goid_important] - -snp_set_size=c(50,100,200,1000) -random_gfb_pred=rep(list(list()),length(snp_set_size)) -names(random_gfb_pred)=names(snp_set_size) -j=1 -for(s in snp_set_size) -{ - random_L2_2_gfblup_prediction_all=readRDS(file=gsub("[[:blank:]]", "", paste("/mnt/LTR_userdata/faroo002/arabidopsis/GP/GFBLUP/random_snp_sets/L2_2_gfblup_prediction_all_",s,".rds"))) - no_of_repeats=length(random_L2_2_gfblup_prediction_all) - for(r in c(1:no_of_repeats)) - { - if(length(random_L2_2_gfblup_prediction_all[[r]]$accuracy$Corr)>0) - { - random_gfb_pred[[j]]<-c(random_gfb_pred[[j]],as.list(random_L2_2_gfblup_prediction_all[[r]]$accuracy$Corr)) - } - } - random_gf=na.omit(unlist(random_gfb_pred[[j]])) -j=j+1 -} -boxplot(unlist(random_gfb_pred[[1]]), -unlist(random_gfb_pred[[2]]), -unlist(random_gfb_pred[[3]]), -unlist(random_gfb_pred[[4]]), -unlist(gfb_pred_important[[1]]), -unlist(gfb_pred_important[[2]]), -unlist(gfb_pred_important[[3]]), -unlist(gfb_pred_important[[4]]), -unlist(gfb_pred_important[[5]]), -xlab="Gene ontology vs random SNP sampling", -ylab="Predictive ability", -names=c(snp_set_size,L2_2_all_important[,11]), -main="Predictive ability using random SNP subsets vs GO based subsets") -#################################################################################################################### diff --git a/code/using_GO/run_models.R b/code/using_GO/run_models.R index 2b54de282e75c5bbfc1fef87b03ccaf30dc28b6f..ed3786d3f572c5b3237b96cc055f3bfc5de58509 100644 --- a/code/using_GO/run_models.R +++ b/code/using_GO/run_models.R @@ -1,4 +1,23 @@ -cd /mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/ +################################################################################################################################## +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} +setwd(paste0(wdir,"/",wd)); +################################################################################################################################## + Rscript psii/H1_1_gblup_vs_gfblup_using_go_model_1_1000.R Rscript psii/H1_1_gblup_vs_gfblup_using_go_model_1001_2000.R Rscript psii/H1_1_gblup_vs_gfblup_using_go_model_2001_3000.R @@ -483,4 +502,4 @@ Rscript pla/T20_2_4001_5000.R Rscript pla/T20_2_5001_6000.R Rscript pla/T20_2_6001_7297.R -pla/8fold/combine.R +Rscript pla/8fold/combine.R diff --git a/code/using_GO/test.R b/code/using_GO/test.R new file mode 100644 index 0000000000000000000000000000000000000000..e00d39731b98975db9f8e0bb3c448c6d53422a8b --- /dev/null +++ b/code/using_GO/test.R @@ -0,0 +1,21 @@ +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$path) +}else{ + wdir <- getwd() +} +this_file = gsub("--file=", "", commandArgs()[grepl("--file", commandArgs())]) +if (length(this_file) > 0){ + wd <- paste(head(strsplit(this_file, '[/|\\]')[[1]], -1), collapse = .Platform$file.sep) +}else{ + wd <- dirname(rstudioapi::getSourceEditorContext()$path) +} +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +setwd(paste0(wdir,"/",wd)); +#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +print(getwd()) \ No newline at end of file