[R] looping problem

[greg holly]

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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>>
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>>

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