looping problem
Thanks so much Peter. I do appreciate for this. Greg
On Thu, Feb 2, 2017 at 10:28 AM, PIKAL Petr <petr.pikal at precheza.cz> wrote:
Hi. Your messages are rather confusing. Well, if you could get correct final data.frame in loop why not just add inside of loop new column(s) by psT$chr <- i Maybe it is time to read R intro as good source for starting with R. It has about 100 pages, but you can pick as start only pages 2-40 which are basic for data input and manipulation. Cheers Petr
-----Original Message----- From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of greg
holly
Sent: Thursday, February 2, 2017 4:13 PM To: Rui Barradas <ruipbarradas at sapo.pt> Cc: r-help mailing list <r-help at r-project.org> Subject: Re: [R] looping problem Thanks so much for this. Unfortunately, cbind did not work. Basically, I
like to
put an extra column named "chr" in the combined file from 22 chr. So chr colum will be "1" for the portion of chr1 in the combined file, 2
for the
portion of chr2 in the combined file and so on. Regards, Greg On Thu, Feb 2, 2017 at 9:39 AM, Rui Barradas <ruipbarradas at sapo.pt>
wrote:
Hello, If I understand correctly, just use ?cbind. Rui Barradas Em 02-02-2017 13:33, greg holly escreveu:
Hi Rui;
Is there any way to insert the chr ids in numeric as 1,2......,22 in
the final output. Here is output from str(temp). So I need also chr
ids in a column.
1 rs58108140 10583 G A -0.070438 0.059903
2 rs189107123 10611 C G -0.044916 0.085853
Regards,
Greg
On Wed, Feb 1, 2017 at 1:32 PM, Rui Barradas <ruipbarradas at sapo.pt
<mailto:ruipbarradas at sapo.pt>> wrote:
Hello,
If what you want is to combine the files into one data.frame then
there are 2 things you should see:
1) You create a variable named 'temp' and don't ever use it.
2) You never combine the data.frames you read in.
Try instead the following.
temp <- data.frame()
for(i in 1:22) {
infile<-paste("chr",i,"/Z-score.imputed",sep="")
psT<-read.table(infile,header=T,as.is <http://as.is
=T,sep="\t")
temp <- rbind(temp, psT)
}
str(temp) # to see what you have
Hope this helps,
Rui Barradas
Em 01-02-2017 17:25, greg holly escreveu:
Hi all;
I have 22 directories named chr1, chr2,....,chr22. Each
directory has a
file named "Z-score.imputed". I would like to combine
Z-score.imputed
files into one. I wrote the following loop but did not get any
results.
Your helps are highly appreciated.
regards,
Greg
temp<-c()
for(i in 1:22) {
infile<-paste("chr",i,"/Z-score.imputed",sep="")
psT<-read.table(as.character(infile),header=T,as.is
<http://as.is>=T,sep="\t")
ps<-psT[psT$Var>0.6,]
ratio=nrow(ps)/nrow(psT)
print(ratio)
}
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