[R] looping problem

greg holly mak.hholly at gmail.com
Thu Feb 2 17:32:24 CET 2017


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)
> > >>         }
> > >>
> > >>                  [[alternative HTML version deleted]]
> > >>
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> >
> >       [[alternative HTML version deleted]]
> >
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