From 47f7516506162b3b87b152a6260e03d3f6c538c7 Mon Sep 17 00:00:00 2001 From: faroo002 <muhammad.farooq@wur.nl> Date: Sun, 8 Nov 2020 12:43:21 +0100 Subject: [PATCH] updated --- code/BLUES.R | 3 - code/aggregate_analysis.R | 51 +- code/make_coex_features_all.R | 150 +- code/make_dataset.R | 222 +- code/make_go_features_all.R | 205 +- code/using_COEX/pla/8fold/combine.R | 4869 +++++++++++++++++ ...p_vs_gfblup_using_coexpression_analysis1.R | 26 +- code/using_COEX/psii/8fold/combine.R | 1766 ++++++ ...p_vs_gfblup_using_coexpression_analysis1.R | 26 +- code/using_COEX/run_models.R | 23 +- code/using_GO/pla/8fold/combine.R | 3418 ++++++++++++ code/using_GO/pla/T14_1_1001_2000.R | 62 +- code/using_GO/pla/T14_1_1_1000.R | 62 +- code/using_GO/pla/T14_1_2001_3000.R | 62 +- code/using_GO/pla/T14_1_3001_4000.R | 62 +- code/using_GO/pla/T14_1_4001_5000.R | 62 +- code/using_GO/pla/T14_1_5001_6000.R | 62 +- code/using_GO/pla/T14_1_6001_7297.R | 62 +- code/using_GO/pla/T14_2_1001_2000.R | 62 +- 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62 +- code/using_GO/pla/T19_7_6001_7297.R | 62 +- code/using_GO/pla/T19_8_1001_2000.R | 62 +- code/using_GO/pla/T19_8_1_1000.R | 62 +- code/using_GO/pla/T19_8_2001_3000.R | 62 +- code/using_GO/pla/T19_8_3001_4000.R | 62 +- code/using_GO/pla/T19_8_4001_5000.R | 62 +- code/using_GO/pla/T19_8_5001_6000.R | 62 +- code/using_GO/pla/T19_8_6001_7297.R | 62 +- code/using_GO/pla/T20_1_1001_2000.R | 62 +- code/using_GO/pla/T20_1_1_1000.R | 62 +- code/using_GO/pla/T20_1_2001_3000.R | 62 +- code/using_GO/pla/T20_1_3001_4000.R | 62 +- code/using_GO/pla/T20_1_4001_5000.R | 62 +- code/using_GO/pla/T20_1_5001_6000.R | 62 +- code/using_GO/pla/T20_1_6001_7297.R | 62 +- code/using_GO/pla/T20_2_1001_2000.R | 62 +- code/using_GO/pla/T20_2_1_1000.R | 62 +- code/using_GO/pla/T20_2_2001_3000.R | 62 +- code/using_GO/pla/T20_2_3001_4000.R | 62 +- code/using_GO/pla/T20_2_4001_5000.R | 62 +- code/using_GO/pla/T20_2_5001_6000.R | 62 +- code/using_GO/pla/T20_2_6001_7297.R | 62 +- .../pla/gblup_vs_gfblup_using_go_analysis1.R | 20 +- code/using_GO/psii/8fold/combine.R | 1258 +++++ .../psii/gblup_vs_gfblup_using_go_analysis1.R | 58 +- code/using_GO/run_models.R | 23 +- code/using_GO/test.R | 21 + 366 files changed, 25779 insertions(+), 8060 deletions(-) create mode 100644 code/using_COEX/pla/8fold/combine.R create mode 100644 code/using_COEX/psii/8fold/combine.R create mode 100644 code/using_GO/pla/8fold/combine.R create mode 100644 code/using_GO/psii/8fold/combine.R create mode 100644 code/using_GO/test.R diff --git a/code/BLUES.R b/code/BLUES.R index c497179..9597e3c 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 d4f8b73..98c25d1 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 4e04ad3..d14f077 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 f8dfb3d..442d378 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 e705738..acec39f 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 0000000..3dad55a --- /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 2e82e61..816f0dc 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()$path) +} +setwd(paste0(wdir,"/",wd,"/8fold/")); +################################################################################################################################## +all_coexpression_clusters <-as.data.frame(read.table(file ="../data/priors/coexpression/ath_gene_clusters.txt", header=TRUE, sep="",strip.white=TRUE)) +coex_markers_number=readRDS(file="../data/priors/coexpression/coex_markers_number.rds") +coex_markers=readRDS(file="../data/priors/coexpression/coex_markers.rds") ################################################################################################################################### T20_2_gblup_variances_all=readRDS(file="./T20_2_gblup_variances_all.rds") T20_2_gblup_prediction_all=readRDS(file="./T20_2_gblup_prediction_all.rds") diff --git a/code/using_COEX/psii/8fold/combine.R b/code/using_COEX/psii/8fold/combine.R new file mode 100644 index 0000000..cbc91f9 --- /dev/null +++ b/code/using_COEX/psii/8fold/combine.R @@ -0,0 +1,1766 @@ +################################################################################################################################## +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$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 cdf3923..a6f69d9 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()$path) +} +setwd(paste0(wdir,"/",wd,"/8fold/")); +################################################################################################################################## +all_coexpression_clusters <-as.data.frame(read.table(file ="../data/priors/coexpression/ath_gene_clusters.txt", header=TRUE, sep="",strip.white=TRUE)) +coex_markers_number=readRDS(file="../data/priors/coexpression/coex_markers_number.rds") +coex_markers=readRDS(file="../data/priors/coexpression/coex_markers.rds") ################################################################################################################################### H4_3_gblup_variances_all=readRDS(file="./H4_3_gblup_variances_all.rds") H4_3_gblup_prediction_all=readRDS(file="./H4_3_gblup_prediction_all.rds") diff --git a/code/using_COEX/run_models.R b/code/using_COEX/run_models.R index a53cc2a..48b1b1d 100644 --- a/code/using_COEX/run_models.R +++ b/code/using_COEX/run_models.R @@ -1,4 +1,23 @@ -cd /mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_COEX +################################################################################################################################## +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$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 0000000..0be7b87 --- /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 5e317bd..76efe84 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 9516a0f..403c8bd 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 2313921..e2b6874 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 8ac39a5..9a40589 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 3e47124..81ca77f 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 eeed787..4c4debc 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 7697a44..b00fe79 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 5a11ab6..fc02a47 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 e4d1021..be9ef7e 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 f1414c6..74c9f92 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 ae553ea..0ad0b08 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 97de7ee..331d3c9 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 fc38029..118bdf2 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 1e2fb34..23065af 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 d39f3ac..f323f91 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 e88f5c0..4a66d73 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 151fff0..8711683 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 8cc719c..93b77d9 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 7100d15..4a37308 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 26e941c..233ff21 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 9130398..4b4c77e 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 3e4419d..4168ad3 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 fb82682..dcd8e92 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 6bd2e0b..7af88f5 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 7ab7605..2e82b0a 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 5a05ccb..d81659e 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 8a992cf..a493ada 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 0c0e0e5..4fd17e2 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 6f75e58..3b71ca4 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 6118957..214e6c3 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 a5b4328..2239b92 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 87343d1..fca111e 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 a43c6db..eb00f67 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 d6df895..7de5864 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 4308141..a0d7956 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 615caa4..86e67e3 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 49aa03e..3b1a8c1 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 c6cbc4c..45c9f76 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 6fa0004..53208ca 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 5ff2b56..1c2b54e 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 e9bc5e0..d9d2f5d 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 c3c71cc..9f23b4e 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 fb02a3a..c634197 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 56d9307..3544e74 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 ec3844f..73c0600 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 59ca235..a3de9fb 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 a9742f2..975a04f 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 2a794aa..d25c511 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 378da97..3a3a18d 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 2b24837..bbfb37e 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 7c10b96..71896ad 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 723ac35..ea91644 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 5d2d962..85697e5 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 0000231..9be86c0 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 ff599fc..16f0677 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 3a0790d..98dabdf 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 3906677..79d3f61 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 461709b..96fa54a 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 ef4eac4..7eb18f5 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 3a101f1..73535a6 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 8258197..10ca074 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 d5998cf..2b0d451 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 27cae6a..dfe215a 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 708769f..71dd7c7 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 05caeeb..d321b2b 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 defc899..234cf08 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 4eac70c..18bcb38 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 fbac682..ed9f208 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 37ee8d4..452ba5c 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 036845f..6337c5c 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 022bfcc..0df2773 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 28741e3..21bd8ee 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 06b102d..e3aba60 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 24a12e5..71e8c19 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 ab79059..9a4110e 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 40ca42f..ca08ede 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 b9945bc..d1b50dd 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 2b4d312..78002b6 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 056cb6b..cfa5af2 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 8e4e371..1e244f2 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 21bb254..d55b5cd 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 37fedac..532b14f 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 5c474ab..e8957c6 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 6b4e58e..d9018c3 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 f2ffdac..db47e64 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 566bf79..3d637b3 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 d7f1909..c20aa25 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 c4dc648..b031116 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 949ffc1..c7472df 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 49e9a78..8a8f8a5 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 e93c701..1fa2d54 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 6e615e7..b1a51a0 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 c302bb2..85b8efc 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 36197e0..c5b57bd 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 42c1875..446cb3f 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 760db50..5d4ed08 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 b23f2ac..5114d92 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 78c2aee..96e8c78 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 c0786b9..2a39ba2 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 86ba4bc..79d628a 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 4c7d977..4655add 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 49a5a81..c7186ef 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 824c878..5696c58 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 92c45f8..fbb5564 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 58ee2a3..70658ef 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 a903e50..1943005 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 29b7426..e8bd77b 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 8e9ff54..3b7e215 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 098466e..1a9215b 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 8c0f44c..1123714 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 6b7141f..eb806fa 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 94a92df..e7ae6b4 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 15c58c9..87f433d 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 5859c7d..ef8a83a 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 b98a17a..5eee3a8 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 d50b026..543b440 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 9b96548..383b304 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 8e3db7d..298fee2 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 136d48f..f0bfa49 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 e7d6af6..bdcef89 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 b18897d..e1c836c 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 69c45b4..9198413 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 8c47046..e0a2093 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 78ed0a3..963d553 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 ffb62ea..51b9d06 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 20f381b..e5dca94 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 0c2b84f..e1c2286 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 3eef118..c093d4c 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 d84db56..6bb1d82 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 6164a25..0b6349b 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 95234f4..edf0b8f 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 13231fc..5722cb4 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 9df06b4..b19bd5e 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 e0d44ef..45c55fb 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 5cd0a6a..88c17b0 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 0f6358c..177dff6 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 ed80345..b38d7c7 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 af19553..a911201 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 6f9695b..ccde480 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 83f9c5e..f4288b0 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 ff653c6..291bcaa 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 4d3c582..e8e1922 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 7c24bf9..370666f 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 ca125a1..29434ef 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 51fb1d5..f1058c6 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 8c07cb0..26423fd 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 5f8f3a1..0c460ff 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 fb207ad..5a4c3cb 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 dcabdb7..eea5b2a 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 8fc0e62..f56010d 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 38e7f57..335c918 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 7dd77a0..879695e 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 0d1b710..c460fdf 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 803624b..2476534 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 a39cc0c..9da9b13 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 a39d072..d4b8ccf 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 bab3ffc..4de6071 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 57956bd..b10199f 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 4316185..7001304 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 97b4439..3ac02ed 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 db9166b..9f97f20 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 79d4a6a..8a4db13 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 781b0fa..b7b4154 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 f1a1c6c..158fff1 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 1969932..e7a9ed4 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 13cd2b5..ca097de 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 02ed2cb..64ec4da 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 af6422c..de02610 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 4d1f06a..96285d7 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 f1828d5..766237a 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 3fa741e..45fe912 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 c780745..9aaa571 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 b21d591..052c104 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 d3b15f2..6672414 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 d99c215..ecfd9bd 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 c9ab357..20f7f48 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 21c3638..b96ef0e 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 1b5235f..5c50053 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 9bb7650..471cb6f 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 9bc8e48..2ab0401 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 d83851d..a8da5fa 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 d39f74a..be45dd3 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 92fb346..e91dea6 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 dd3f119..4d67879 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 5896ef5..74154a0 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 d0e95d1..2e6035a 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 bf5c72d..6a74a7b 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 5a87115..2ff4120 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 e8732e5..6ba5d85 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 19cd99b..9f0778f 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 cc87926..bc5c859 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 5eb4e62..4624372 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 edf1dfb..861ef2c 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 9f1b98f..c9b79c0 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 d3f9d0a..549b5d6 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 b773a9c..dc72a19 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 6adad76..51ec6e8 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 d423904..3948b76 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 365c4ca..84cd259 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 5a70ee4..8368d79 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 fbd7400..2831d3b 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 f6d90f2..32d59de 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 94e5775..2158e86 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 6c041cd..56e99b6 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 46860ae..004148e 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 41e9f52..09fc419 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 165d60b..295532f 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 abe1608..15a3fe1 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 96c1530..84cedac 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 f21d37b..2d5c201 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 0482886..376a81f 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 bfcf41e..a4ace90 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 732e7ff..3290f13 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 9903532..0aaf4d1 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 cf0bd60..4619e5f 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 7ea3049..39e4cb6 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 aeda6a2..b4ce0fe 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 4484afb..8d49cce 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 17ff577..c530429 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 d35a28b..957b532 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 97ac630..52f95be 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 343dbb0..656a0cf 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 0cef780..6b1bb26 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 a433111..e422447 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 e395a94..3d15255 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 aa48c3c..1984618 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 8cc1b22..eec0015 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 bbd0e59..81459db 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 0020d41..3c367ff 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 21fb218..ce134bb 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 f9bbf65..409c3eb 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 49d5979..3a1a699 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 a33fe9d..7ec0f92 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 b69edc8..cd1d13e 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 a29a303..e82c87b 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 239fdb6..a379f08 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 95143f4..078e020 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 8d7216d..b352c2f 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 5e541d7..7267804 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 5a28208..4c135b8 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 d1d57df..0e14976 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 7209106..387fcf7 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 600b5b1..abc2365 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 dddf977..27cd698 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 b2ad2eb..f54c0d9 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 f3f2b96..55a008c 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 287f784..3fa26c6 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 c6212a6..e7befd5 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 33598de..84beee8 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 1dbce5c..c5affc9 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 ec1a8a0..d1d82bd 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 3827199..0fdc010 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 26fcb78..235a3d8 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 0a36077..599c702 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 29dead9..f2743ff 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 4b7e1ad..ad4ecf8 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 97e3b41..3b2d3b6 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 7983d5c..3f7d951 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 e086244..33a8aa9 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 19a770a..8b11dbe 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 5793c29..59dc1e9 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 dc17a9e..19682ac 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 7c305d4..f7dba2e 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 fd400b7..52e7348 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 6016036..93cd5c5 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 32ed667..718cbd1 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 12d6413..1236569 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 160483d..5b2dc02 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 8a73255..499fe04 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 24a77c8..9be5a1f 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 eb76ec9..1e805e3 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 eb898ff..10bea6c 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 8d9de36..a7c8db8 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 198b007..cf9db30 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 bce9d22..5d77d1f 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 6272077..d21531a 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 5f09c03..43bd8fd 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 9b870c8..d5dd96d 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 efe52ac..9e29a3d 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 e91b2ed..83c1e61 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 a24d3bd..4012789 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 df74bb6..075cdb9 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 9993149..53ba190 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 3acc5e8..83b4677 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 c1f7390..b153928 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 43fe40c..635bff5 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 b5653ad..d0fb5c1 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 32966c1..eb9a0e1 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 6921cb1..a96c3f0 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 dd72470..d3710a7 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 37815c8..c7fae60 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 086a394..f6ff6a5 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 7633b44..fccf2f7 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 76fed4e..a2af490 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 157a4b4..fbd925c 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 692b823..aefa6e7 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 8962a1d..9199651 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 e09750c..d2d86f3 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 8daf777..0138bc7 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 4305ce8..54d5b56 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 ade8f19..57b0788 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 afebbb4..8b04bd9 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 2e215a5..51503d0 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 729ace8..349dc21 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 6bf9e07..79ac4e9 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 5686a5e..6870955 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 5917ed4..c894e02 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 8157130..721057e 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 d45a199..edae8dd 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 f5ff7ca..a9d8923 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 357aafd..0e693b4 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 8d1ab5c..2af97cd 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 af4cb87..a62ddf3 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 3c1a372..aa285dc 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 f6970db..283aa3a 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 0b6396c..9c4755f 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 4962934..fe92f7d 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 e89602d..49091aa 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 6abad1e..696be87 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 de6adc4..5592ea6 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 9af25ae..8d3f588 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 06492fb..c98cce2 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 c8d6c10..cf36af3 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 450a7ef..e48d3e7 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 7cb6b03..4e2b8ed 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 bffea95..eda96da 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 f3ff484..1b91da2 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 0d79810..d496d98 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 9d812e2..dcd1945 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 ea6b791..5f5c01e 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 e545504..cec93bb 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 d87af76..b3e0edc 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 9822cbc..6f8b04d 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 4a5b40a..a6a8c95 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 766d4f8..6a09d14 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 c699d86..8a3e143 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 e4f24a8..2027d48 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 7b0d3d3..b683a67 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 dac8bf8..8ab5747 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 789b040..c14f8a6 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 4a8b356..8863913 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 ed86247..7228e43 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 ce3fb32..b7df920 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 7242215..6fe0f91 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 ada4b08..a376915 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 5dbc48d..b472bad 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 0824607..82f45c0 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 fe263e2..a88e2bc 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 d10b150..d7bedd4 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 0b0f475..2b8eac6 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 b950c2c..a96dbba 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()$path) +} +setwd(paste0(wdir,"/",wd,"/8fold/")); +################################################################################################################# + require(GO.db) T20_2_gblup_variances_all=readRDS(file="./T20_2_gblup_variances_all.rds") diff --git a/code/using_GO/psii/8fold/combine.R b/code/using_GO/psii/8fold/combine.R new file mode 100644 index 0000000..374cd42 --- /dev/null +++ b/code/using_GO/psii/8fold/combine.R @@ -0,0 +1,1258 @@ +################################################################################################################################## +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$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 e02a732..e0cc750 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$Corr)) - } - } - random_gf=na.omit(unlist(random_gfb_pred[[j]])) -j=j+1 -} -boxplot(unlist(random_gfb_pred[[1]]), -unlist(random_gfb_pred[[2]]), -unlist(random_gfb_pred[[3]]), -unlist(random_gfb_pred[[4]]), -unlist(gfb_pred_important[[1]]), -unlist(gfb_pred_important[[2]]), -unlist(gfb_pred_important[[3]]), -unlist(gfb_pred_important[[4]]), -unlist(gfb_pred_important[[5]]), -xlab="Gene ontology vs random SNP sampling", -ylab="Predictive ability", -names=c(snp_set_size,L2_2_all_important[,11]), -main="Predictive ability using random SNP subsets vs GO based subsets") -#################################################################################################################### diff --git a/code/using_GO/run_models.R b/code/using_GO/run_models.R index 2b54de2..ed3786d 100644 --- a/code/using_GO/run_models.R +++ b/code/using_GO/run_models.R @@ -1,4 +1,23 @@ -cd /mnt/LTR_userdata/faroo002/arabidopsis/GP/using_conda/using_GO/ +################################################################################################################################## +if (rstudioapi::isAvailable()) { + if (require('rstudioapi') != TRUE) { + install.packages('rstudioapi') + }else{ + library(rstudioapi) # load it + } + wdir <- dirname(getActiveDocumentContext()$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 0000000..e00d397 --- /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 -- GitLab