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.
?list.files
(Which also has pattern matching facilities through its second
argument.)
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?
--
David.
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.hug...@bath.ac.uk
http://www.bath.ac.uk/bio-sci/biodiversity-lab/hughes.html
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David Winsemius, MD
West Hartford, CT
______________________________________________
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
