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#!/usr/bin/env Rscript
args<-commandArgs(TRUE)
if (length(args) == 0) {
stop("usage: validate_UP_subset.Rscript samples.txt");
}
samples_txt_file <- args[1]
validate_UP_subset <- function(filename, samples_list) {
cat("validating: ", filename, "\n")
data <- read.table(filename, header=T, stringsAsFactors=F)
if (nrow(data) == 0) {
message("no DE entries reported here.")
return(0)
}
sampleA <- data[['sampleA']][1]
sampleB <- data[['sampleB']][1]
sampleA_rep_names <- samples_list[[sampleA]][['replicate']]
sampleB_rep_names <- samples_list[[sampleB]][['replicate']]
sampleA_idx <- which(colnames(data) %in% sampleA_rep_names)
sampleB_idx <- which(colnames(data) %in% sampleB_rep_names)
sampleA_mean <- apply(data, 1, function(x) mean(as.numeric(x[sampleA_idx])))
sampleB_mean <- apply(data, 1, function(x) mean(as.numeric(x[sampleB_idx])))
cat("sampleA_mean: ", sampleA_mean, "\n")
cat("sampleB_mean: ", sampleB_mean, "\n")
num_discordant <- sum(sampleA_mean/sampleB_mean < 0)
cat("num discordant: ", num_discordant, "\n")
return(num_discordant)
}
samples_info <- read.table(samples_txt_file, stringsAsFactors=F)
colnames(samples_info) <- c('sample', 'replicate')
samples_list <- split(samples_info, samples_info$sample)
files <- dir(pattern="*-UP.subset$")
errflag <- 0
for (file in files) {
num_discordant <- validate_UP_subset(file, samples_list)
if (num_discordant > 0) {
errflag <- 1
warning("File: (", file, ") has ", num_discordant, " discordant features")
}
else {
message("File: (", file, ") passes test.")
}
}
quit("no", errflag)
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