[R] R shell script

[Steve Lianoglou]

Hi,

On Wed, Apr 25, 2012 at 11:11 AM, aoife doherty
<aoife.m.doherty at gmail.com> wrote:
> 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?

In this case, just make your function write a text file -- you have to
figure out what you want to save and serialize it to text. Or you can
write as many output rds (or rda) files as you do tests, for instance:

filez <- list.files(pattern="*.out")
for (f in filez) {
  ## something to load the data in file `f` I presume
  w <- wilcox.test(... on the data you loaded ...)

  saveRDS(w, gsub('.out', '.rds', f) ## if you want to save the object
}

or
info <- lapply(filez, function(x) {
  ## load the file
  w <- wilcox.test(... on the data you loaded ...)
  data.frame(file.name=x, statistic=w$statistic, p.value=w$p.value,
... anything else you want?)
})
result <- do.call(rbind, info)
write.table(result, 'wilcox.results.txt', ...)

HTH,
-steve

>
>
>
> On Wed, Apr 25, 2012 at 4:03 PM, R. Michael Weylandt <
> michael.weylandt at 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 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]]
>> >
>> > ______________________________________________
>> > R-help at 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]]
>
> ______________________________________________
> R-help at 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.



-- 
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