Thanks for replying.

My problem is that i have say 50 input files, that i wanted to run a
particular command on, get 50 output files, and then when i close R, have
them in my directory?

so for example if i say:

>R

>library(MASS)

>list.files(pattern = ".out")

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

<<<send each output to a different file, and save it in such a way that
when i close R the outputs are still there>>>

i thought this might be easier in a shell way?



On Wed, Apr 25, 2012 at 4:03 PM, R. Michael Weylandt <
michael.weylandt@gmail.com> wrote:

> 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@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]]
> >
> > ______________________________________________
> > R-help@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
>

	[[alternative HTML version deleted]]

