might be the way to go. That's what we did :-)
Of course, if you have a file with the plink commands already stored as a script, you can always
system('bash script_file.sh'). For this to work in an automated though, you would need to address changing input parameters on the fly within the script file, at which point it becomes easier to just construct the command as a string and execute that string instead of adding on a couple of File IO operations.