From 44ff4c0a1bd425ca331ac1db4b301d90378d7069 Mon Sep 17 00:00:00 2001
From: Hartanto <margi.hartanto@wur.nl>
Date: Wed, 19 Feb 2020 17:07:35 +0100
Subject: [PATCH] add procedure to calculate the average rank of genes over
different threshold
---
5-create-community-network.R | 31 +++++++++++++++++++++++++++----
1 file changed, 27 insertions(+), 4 deletions(-)
diff --git a/5-create-community-network.R b/5-create-community-network.R
index cc387f6..e0e1ebc 100644
--- a/5-create-community-network.R
+++ b/5-create-community-network.R
@@ -22,10 +22,10 @@
library(Hmisc)
# determine the stage and transband ####
- dev.stage <- 'im'
+ dev.stage <- 'rp'
chr <- 5
- start <- 6000000
- end <- 8000000
+ start <- 24000000
+ end <- 26000000
n.perm <- 1000
# load required data ####
@@ -291,7 +291,30 @@
plot(threshold.m$threshold,
threshold.m$node,
xlab = "rank threshold",
- ylab = 'number of node') # 1552 for RP5 and 1248 for PD3
+ ylab = 'number of node') # 1552 for RP4 and 1248 for PD2
+
+ # determine the stability of rank (RP4)
+
+ degree.table <- data.frame(candidates = candidates)
+
+ for(i in max(round(edges$interaction, 0)):1) {
+ print(i)
+ edge.thresholded <- filter(edges, interaction <= i)
+ degree.table.tmp <- as.data.frame(table(edge.thresholded$source))
+ colnames(degree.table.tmp) <- c("candidates", i)
+ rank.degree.table <- merge(data.frame(candidates = candidates),
+ degree.table.tmp, all.x = T)
+ rank.degree.table$rank <- rank(-rank.degree.table[, 2],
+ na.last = T, ties.method = 'average')
+ degree.table[, paste0(i)] <- rank(-rank.degree.table[, 2],
+ na.last = T, ties.method = 'average')
+ }
+
+ all.rank <- data.frame(candidates,
+ mean = round(apply(degree.table[2:ncol(degree.table)], 1, mean), 2),
+ sd = round(apply(degree.table[2:ncol(degree.table)], 1, sd), 2))
+ all.rank <- all.rank[order(all.rank$mean), ]
+ write.csv(all.rank, paste0('networks/', dev.stage, chr, '-ranks.csv'))
# visualize the network
edges.th <- filter(edges, interaction <= 288)
--
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