cbind with row names to spliting by Chr in R

Question

[viniciushs88]

I would like to use the cbind in a list of files. However each file are split in a specific chromosome (chr) (k in 1:29), and specific sample (i in 1:777). The files are like:

sample1chr1.txt, sample1chr2.txt ... sample1chr29.txt, sample2chr1.txt ... sample777chr29.txt

All files have exactly the same rows names (3 first columns represent my row names). I would like to get a final file to each chr merging to all sample files, with and do not repeat the row names in the final file (the first 3 columns representing my rows names).

I tried this:

#Creating file with row names (3 first columns) to each Chr
{
{for(k in 1:29){
  infile <- paste0("sample1chr",k,".txt")
  outfile <- paste0("LRRrawallchr",k,".txt")
  rows <- read.table(infile, header=TRUE, sep="\t")
  rows <- rows[, -grep("Log.R.Ratio", colnames(rows))]
  write.table(rows, outfile, sep=";")}}

#Cbind in one file per Chr
{  for(i in 1:777)
  for(k in 1:29)
    base <- paste0("LRRrawallchr",k,".txt")
    chr <- read.table(base, header=TRUE, sep=";")
    infile <- paste0("sample",i,"chr",k,".txt")
    chr2 <- read.table(infile, header=TRUE, sep="\t")
    outfile <- paste0("LRRrawallchr",k,".txt")
    chr2 <- chr2[, -grep("Name", colnames(chr2))]
    chr2 <- chr2[, -grep("Chr", colnames(chr2))]
    chr2 <- chr2[, -grep("Position", colnames(chr2))]
    chr <- cbind(chr, chr2)
    write.table(chr, outfile, sep=";", row.names=FALSE, col.names=FALSE)}
}

In the end I just get the 3 columns representing my row names and just one column with values (4 column in all sample input files) Cheers!

[Michael]

I doubt that all your files have identical row-names because the chromosomes are different.

[viniciushs88]

All sample files to a same Chr have. In the end I expect 29 final files (one per Chr). I wanna o ´cbind´ all values (4 collum in input files), separately to each Chr.

I have 22553 diferent .txt files (29 files (one per chr) to each of 777 samples).

[Devon Ryan]

This is really not a good example of a problem that R is designed for. Is there a reason you don't want to use python or perl or even C (all of which would perform vastly better)?

[Ido Tamir]

If this is really your code maybe you just miss one pair of parentheses around the inner for loop?