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
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