[R] looping problem

Thu Feb 2 16:28:58 CET 2017

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)
> >>         }
> >>
> >>                  [[alternative HTML version deleted]]
> >>
> >>         ______________________________________________
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> >>         <https://stat.ethz.ch/mailman/listinfo/r-help>
> >>         PLEASE do read the posting guide
> >>         http://www.R-project.org/posting-guide.html
> >>         <http://www.R-project.org/posting-guide.html>
> >>         and provide commented, minimal, self-contained, reproducible code.
> >>
> >>
> >>
>
>       [[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
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> PLEASE do read the posting guide http://www.R-project.org/posting-
> guide.html
> and provide commented, minimal, self-contained, reproducible code.

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