R help - May 2011 - quick question : interpolating file name in pipe command

Hi Guys

I am trying to read a bunch of files in the loop but pipe function
which I use to cut few columns is somehow unable to interpolate the
file variable.


eg:
> file="check.txt"
> data  <- read.table(pipe("cut -f 2,3 file"),
sep="\t", col.names=c('pos','cov') )
cut: file: No such file or directory

how can I pass variable file to pipe so that it can be interpolated.

Thanks!
-Abhi

You can ignore my question I was able to figure out the way. I guess
when I touch R after couple of weeks I am rusty.



-Abhi

On Thu, May 5, 2011 at 2:15 PM, Abhishek Pratap <abhishek.vit at
gmail.com> wrote:
> Hi Guys
>
> I am trying to read a bunch of files in the loop but pipe function
> which I use to cut few columns is somehow unable to interpolate the
> file variable.
>
>
> eg:
>
>> file="check.txt"
>> data ?<- read.table(pipe("cut -f 2,3 file"),
sep="\t", col.names=c('pos','cov') )
> cut: file: No such file or directory
>
> how can I pass variable file to pipe so that it can be interpolated.
>
> Thanks!
> -Abhi
>

On May 5, 2011, at 5:15 PM, Abhishek Pratap wrote:
> Hi Guys
>
> I am trying to read a bunch of files in the loop but pipe function
> which I use to cut few columns is somehow unable to interpolate the
> file variable.
>
>
> eg:
>
>> file="check.txt"
>> data  <- read.table(pipe("cut -f 2,3 file"),
sep="\t",
>> col.names=c('pos','cov') )
I do not see where you allowed the substitution of the character  
vector file into the pipe argument.
Perhaps:

data  <- read.table(pipe(paste("cut -f 2,3", file)),
sep="\t",
col.names=c('pos','cov') )

(Bad practice to name variables "file".)

I didn't use tabs but rather spaces:

check.txt was a single line file

ttt tt rr ttt

 > data  <- read.table(pipe(paste("cut -f 2,3", file)),   
col.names=c('pos','cov') )
 > data
   pos cov
1 ttt  tt
2  rr ttt
> cut: file: No such file or directory
>
> how can I pass variable file to pipe so that it can be interpolated.
>
> Thanks!
> -Abhi
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
David Winsemius, MD
West Hartford, CT