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looping problem

8 messages · greg holly, Rui Barradas, PIKAL Petr

greg holly
# 
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=T,sep="\t")
ps<-psT[psT$Var>0.6,]
ratio=nrow(ps)/nrow(psT)
print(ratio)
}
Rui Barradas
# 
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=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:
greg holly
# 
Hi Rui;

I do appreciate for this. Thanks so much. I will try ASAP.

Regards,

Greg
On Wed, Feb 1, 2017 at 1:32 PM, Rui Barradas <ruipbarradas at sapo.pt> wrote:

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      greg holly
    

    

      
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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> wrote:

        

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Rui Barradas
    

    

      
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Hello,

If I understand correctly, just use ?cbind.

Rui Barradas

Em 02-02-2017 13:33, greg holly escreveu:

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      greg holly
    

    

      
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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:

        

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      PIKAL Petr
    

    

      
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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

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

        
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      greg holly
    

    

      
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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: