[R] many datasets run with one R script in a computer cluster

David Winsemius dwinsemius at comcast.net
Fri Oct 8 20:30:14 CEST 2010

On Oct 8, 2010, at 12:33 PM, Martin Hughes wrote:

> Hello Everyone
> I have an R script (and a source file which I keep my functions)  
> that I need to run on 70 data sets (each consisting of a pair of  
> files).
> I wish to run these data sets in a computer cluster that is run by  
> my uni (HOWEVER they cannot help me with this problem but say it is  
> do-able)
> the cluster is clever enough that if i set my data up as follows:  
> within one folder called 'work' there is 70 subfolders each of which  
> contain a pair of files, each pair of files having a unique first  
> part eg CottonEA05 as in the example text below)
> then if I have one R script to run the analysis within the main  
> folder, it will open each subfolder, run the R script and output the  
> results into that subfolder.
> The problem is that this script for R needs to have some kind of  
> wild card element so for example in the script below, R will replace  
> CottonEA05 with the whatever the unique identifier is for the  
> particular subfolder its looking through eg change it to   
> Martin_M_STAGE.txt or bananas_M_STAGE.txt etc
> Can R do this? ie can it look a file title, and change the file name  
> within the script to be the same as that file title, and then run  
> the analysis

It can certain read a directory and return the file names into a  
vector. And you can certainly do sub() on that vector to strip out the  
leading characters before the first occurrence of a character.


(Which also has pattern matching facilities through its second  

This reads the files in my working directory and then returns only the  
characters before the first period:

 > filist <- list.files()
 > str(filist)
  chr [1:295] "_train_1.dat" "~Show.Dot.Files.txt" ...
 > first <- sub("\\..+$","", filist)
 > str(first)
  chr [1:295] "_train_1" "~Show" "~UCONN" "2001VBTANB" ...

Was that what you were asking?


> OR do I have to use another programme that does that?
> ###
> m<-read.table("CottonEA05_M_STAGE.txt")
> #"CottonEA05" what is different for each dataset
> M<-as.matrix(m[,-c(1)])
> rownames(M)<-(m[,1])
> pa<-read.table("CottonEA05_D_STAGE.txt",header=T)
> timetable<-read.table("TimeBinLookup.txt",header=T,sep="\t")
> PA<-as.matrix(pa[,-c(1)])
> rownames(PA)<-(pa[,1])
> OCHAR<-c()
> source("DISPARITY.R")
> library(calibrate)
> ###
> Thanks
> Martin
> -- 
> Martin Hughes
> MPhil/PhD Research in Biology
> Rm 1.07,  4south
> University of Bath
> Department of Biology and Biochemistry
> Claverton
> Bath    BA2 7AY
> Tel: 01225 385 437
> M.Hughes at bath.ac.uk
> http://www.bath.ac.uk/bio-sci/biodiversity-lab/hughes.html
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> and provide commented, minimal, self-contained, reproducible code.

David Winsemius, MD
West Hartford, CT

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