Hi,
The rownames part is not clear as your expected output and input files didn't
show them as rownames.
##Suppose you have all the files in a folder
##here I am creating the names of those files
files1 <- paste0("sample", rep(1:777, each=29),"chr",1:29,".txt")
length(files1)
#[1] 22533
lst1 <- split(files1,as.numeric(gsub(".*chr(\\d+)\\..*","\\1",files1)))
##use list.files()
##in your case, ##not tested
lst1 <- split(list.files(pattern="sample\\d+"),
as.numeric(gsub(".*chr(\\d+)\\..*","\\1",list.files(pattern="sample\\d+"))))
##in case other files are also in the folder
library(plyr)
lst2 <- lapply(lst1,function(x) {x1 <-join_all(lapply(x,function(y)
read.table(y,header=TRUE,stringsAsFactors=FALSE,sep="")),c("Name","Chr","Position"))
})
lapply(seq_along(lst2),function(i)
write.table(lst2[[i]],paste0("LRRrawallchr",i,".txt"),row.names=FALSE,quote=FALSE))
###if you need to create rownames using the first three columns:
lapply(seq_along(lst2),function(i) {x1 <- lst2[[i]]; row.names(x1) <-
as.character(interaction(x1[,1:3],sep="_")); x2 <- x1[,-(1:3)]; write.table(x2,
paste0("LRRrawallchr",i,".txt"), quote=FALSE)})
A.K.
I would like to use the `cbind` in a list of files. However each file are
splited 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 collumns 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
collumns representing my rows names).
I tried this:
`#Creating file with row names (3 first collumns) 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)}
}`
Input example (sample1chr1.txt):
Name Chr Position sample1value
BAC-11034 1 128 0.302
BAC-11044 1 129 -0.56
BAC-11057 1 134 0.0840
Input example (sample2chr1.txt):
Name Chr Position sample2value
BAC-11034 1 128 0.25
BAC-11044 1 129 0.41
BAC-11057 1 134 -0.14
Expected output (LRRrawallchr1):
Name Chr Position sample1value sample2value
BAC-11034 1 128 0.302 0.25
BAC-11044 1 129 -0.56 0.41
BAC-11057 1 134 0.0840 -0.14
I have 22553 diferent .txt files (29 files (one per chr) to each of 777
samples). All 22553 files (sample1chr1.txt, sample1chr2.txt ...
sample1chr29.txt, sample2chr1.txt ... sample777chr29.txt) are like above
example.
I wanna 29 files like (LRRrawallchr1), one per Chr. The "LRRrawallchr,k," files
have to be with 777+3 (800 collumns). The 3 row names and one collumn per
sample.
Cheers!
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