[R] R shell script

[R. Michael Weylandt]

You can do this in bash but why not just do it in R directly? You probably need

list.files(pattern = ".out")

to get started. Then just wrap your script in a function and pass it
to (s|l)apply something like:

sapply(list.files(pattern  = *.out"), function(x) wilcox.test ( ... ) )

Michael

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
>
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>
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