Calling the R function within the bash script to be run on a cluster

Aemm · 11-22-2018, 01:25 AM

Hi all,
I had a set of files which I split into two (.control and .case) using bash script. Now I want to run the R function "t.test" on it. Is there a way to run/call the R function within the bash script such that the names are stored in variable and I want to use the same name in R function as well. the script which I have right now is

Code:

cd $PBS_O_WORKDIR
for FileName in $(cat Artery_Aorta-ListOfScoreFilesForScript.txt); 
do 
cat "$FileName" | awk -v fn="$FileName" '{if ($3 == 1) {print $6 >>fn".control"} else if ($3 == 2) {print $6 >>fn".case"}}';
Rscript t.test($FileName.control, $FileName.case, alternative = "two.sided", paired = FALSE, var.equal = FALSE)
done;

I also want to output the result of the t.test into the same variable $FileName along with the .test extension.

berndbausch · 11-22-2018, 01:50 AM

Quote:

Originally Posted by Aemm

such that the names are stored in variable and I want to use the same name in R function as well.

Which names, and which name?

Quote:

Originally Posted by Aemm

I also want to output the result of the t.test into the same variable $FileName along with the .test extension.

You mean that you want to output the result to a file named $FileName.test. Correct? If so, just use the greater sign “> $FileName.test” to redirect the output.