[R] R shell script

[Steve Lianoglou]

Check out the vignette for the optparse library:

http://cran.r-project.org/web/packages/optparse/vignettes/optparse.pdf

Super helpful library if you plan on making any semi-interesting
command line scripts w/ R.

-steve

On Wed, Apr 25, 2012 at 6:47 AM, aoife doherty
<aoife.m.doherty at gmail.com> wrote:
> Hey guys,
> Does anyone have an example of a REALLY simple shell script in R.
>
> Basically i want to run this command:
>
> library(MASS)
> wilcox.test(list1,list2,paired=TRUE,alternative=c("greater"),correct=TRUE,exact=FALSE)
>
> in a shell script something like this:
>
> #!/bin/bash
> R
> library(MASS)
> for i in *.out
> do
> wilcox.test($i,${i/out}.out2,paired=TRUE) >> $i.out
> done
>
>
> that i can run on a command line this this:
> sh R.sh
>
>
> because i've SO many files to run this command on.
>
>
> I've been googling, but i'm having trouble of just finding a simple example
> explaining how to make this shell script.
>
> Any help appreciated :)
> Aoife
>
>        [[alternative HTML version deleted]]
>
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-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact