In Bash shell

# a=1
# b=10
# Rscript -e "args<-commandArgs(TRUE);x=args[1]:args[2];x;mean(x);sd(x
+)" $a $b
 [1]  1  2  3  4  5  6  7  8  9 10
[1] 5.5
[1] 3.027650
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So you can control variables on the command line R script and you can feed these variables into R itself using commandArgs(TRUE), and manipulate the variables as args1 and args2. So if I imagine if you are doing a system call in perl, you can also construct a similar Rscript on the command line, and get the output accordingly, which you can manipulate further within perl (or any other script).