Command Line arguments in R

Question

I'd like to know if it's possible to pass a string as a command line argument to execute in R?

I've attempted it already and I think it's parsing based on space, regardless of quotation marks.

./R_Script.r abc.bed def.bed "cat bedgraph 1,2"

Answer 1

It shouldn't be parsing based on space. I'm also not sure why you are trying to execute your R script file directly, rather than using Rscript and passing the script file. If your R_Script.r file contains only one line: commandArgs(), then running this line:

Rscript --vanilla R_Script.r "first second"

should get you:

[1] "/usr/local/lib/R/bin/exec/R" "--slave"
[3] "--no-restore"                "--vanilla"
[5] "--file=R_Script.r"           "--args"
[7] "first second"

As you can see, the 7th element of the list is first second, so it isn't parsing the space.