But may be you will like to feed through pipe both data and commands? It will require to do some formatting of input but I think it will not be hard to do in perl. I mean something like that:

echo "source(\"RCommands.R\");t<-matrix(c(1,2,3,4,5,6),ncol=2);print(process(t))" | R --slave

You only need to substitute your data inside c() with all separators replaced with commas and specify number of columns in your data as ncol=...

Good luck...

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