R/average_pcc_calculations.R

In oacar/pgsNetwork: This package is used for ref

library(tidyverse)
library(igraph)
args <- commandArgs(TRUE)
ndlist1_fname <- args[1]
adj_res1_fname <- args[2]
ndlist2_fname <- args[3]
adj_res2_fname <- args[4]
out_name <- args[5]


ndlist1 <- read_delim(ndlist1_fname,delim='\t',col_names = FALSE)
adj_res1 <- read_delim(adj_res1_fname,delim='\t',col_names=FALSE)
adj_res1 <- as.matrix(adj_res1)
colnames(adj_res1) <- ndlist1$X1
rownames(adj_res1) <- ndlist1$X1
print('adj_res1 is imported')

ndlist2 <- read_delim(ndlist2_fname,delim='\t',col_names = FALSE)
adj_res2 <- read_delim(adj_res2_fname,delim='\t',col_names=FALSE)
adj_res2 <- as.matrix(adj_res2)
colnames(adj_res2) <- ndlist2$X1
rownames(adj_res2) <- ndlist2$X1
print('adj_res2 is imported')
adj_res2 <- adj_res2[rownames(adj_res1),colnames(adj_res1)]


adj_avg <- (adj_res1+adj_res2)/2
adj_avg[is.nan(adj_avg)] <- 0 
print('adj_avg is calculated')
write.table(adj_avg,out_name,col.names=F,sep='\t',row.names=F)
#write.table()
#png('avg.png')
#hist(adj_avg[adj_avg>=0.5])
#dev.off()
#adj_avg[adj_avg>=0.2]