R script for merging Kallisto TPMs from output directories below path given as command-line argument

merge_kallisto_TPM.R

args = commandArgs(trailingOnly=TRUE)
path=args[1]
files=Sys.glob(paste0(path,"/*/abundance.tsv"))
#print(files)
merge_two <- function(x,y){
	  #print(dim(x))
	  if ("tpm" %in% colnames(x)){
	     x_ <- x[,c(1,5)]
	     }
	   else{
		x_ <- x
		}
	  y_ <- y[,c(1,5)]
	  z <- merge(x_, y_, by="target_id")
	  return(z)
}	

read.delim.print <- function(x){
	print(x)
	read.delim(x, header=TRUE)
}

#x <- lapply(files, function(f) read.delim.print(f))
#suppressWarnings(mx <- Reduce(merge_two, x))

ctr = 0
#print(files[1])
mx <- read.delim(files[1],header=TRUE)
for(i in 2:length(files)){
         f2 = files[i]
	 print(paste('Merge', ctr))
	 tmp <- merge_two(mx, read.delim(f2, header=TRUE))
	 mx <- tmp
	 ctr <- ctr + 1
}

rn <- mx[,1]
mx <- mx[-1]
rownames(mx) <- rn
colnames(mx) <- sapply(files, function(x) unlist(strsplit(x, split="/"))[2])

write.table(mx,file="kallisto_TPM.txt",quote=FALSE,sep="\t")

Originally implemented by reading all files into memory and merging by Reduce() applied to merge, this was rewritten to do it file by file due to memory issues on a machine where I tried to do this on 200 samples.

Run by

Rscript merge_kallisto_TPM.R directory above Kallisto output directories