On 21.10.2011 23:32, Debs Majumdar wrote:
Hi,
I have been given a set of around 300 files where there are 5 files
corresponding to each chunk.
E.g. Chunk 1 for chr1 contains these 5 files:
chr1.one.phased.impute2.chunk1
chr1.one.phased.impute2.chunk1_info
chr1.one.phased.impute2.chunk1_info_by_sample
chr1.one.phased.impute2.chunk1_summary
chr1.one.phased.impute2.chunk1_warnings
For chr 1 there are 47 chunks, chr2 has 42 chunks...and it ends at chr22 with
23 chunks.
I am using the DatABEL package to convert them databel format using the
following command:
impute2databel(genofile="chr1.one.phased.impute2.chunk1",
samplefile="chr1.one.phased.impute2.chunk1_info", outfile="chr1.chunk1", makeprob=TRUE,
old=FALSE)
which uses two files per chunk.
Is there a way I can automate this so that the code goes through each chunk of
each chromosome and does the conversion to databel format.
Yes, probably (all untested):
owd <- setwd(pth)
fls <- list.files(pattern="^chr")
ufls <- unique(sapply(strsplit(fls, "_"), "[", 1))
for(i in ufls){
of <- strsplit(i, "\\.")[[1]]
of <- paste(of[1], tail(of, 1), sep=".")
impute2databel(genofile = i,
samplefile = paste(i, "info", sep="_"),
outfile = of,
makeprob=TRUE, old=FALSE)
}
setwd(owd)
Uwe Ligges
Thanks,
-Debs
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and provide commented, minimal, self-contained, reproducible code.
