Thanks Uwe. This works perfectly.
#######
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)
####
I have a question regarding how strsplit works.
When my files are the following:
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
ufls <- unique(sapply(strsplit(fls, "_"), "[", 1))
This works like a charm.
I have another dataset where the files are
study1_chr1.one.phased.impute2.chunk1
study1_chr1.one.phased.impute2.chunk1_info
study1_chr1.one.phased.impute2.chunk1_info_by_sample
study1_chr1.one.phased.impute2.chunk1_summary
study1_chr1.one.phased.impute2.chunk1_warnings
... and so on.
and I wanted to run the same loop but I was unable to change strsplit so that
it will work when the files are names ads above:
I tried
ufls <- unique(sapply(strsplit(fls, "_"), "[", 2))
but this knocks off "study1" (modified code below). What modification do I
need to make to make this run:
####
fls <- list.files(pattern="study1_chr")
ufls <- unique(sapply(strsplit(fls, "_"), "[", 2))
library(GenABEL)
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)
}
#####
Thanks,
Debs
----- Original Message -----
From: Debs Majumdar <debs_st...@yahoo.com>
To: "r-help@r-project.org" <r-help@r-project.org>
Cc:
Sent: Friday, October 21, 2011 2:32 PM
Subject: Reading in and modifying multiple datasets in a loop
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.
Thanks,
-Debs
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