[R] Running R Script on a Sequence of Files

Bert Gunter gunter.berton at gene.com
Fri Dec 5 20:04:05 CET 2008

 R has quite a few functions to get and manipulate filenames to facilitate
exactly what you want to do. See ?files and especially the links at the end
to the file name manipulation functions.

e.g. dir("pathname") lists all file names in the directory "pathname."
?list.files gives details.

-- Bert Gunter

-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On
Behalf Of Chris Poliquin
Sent: Friday, December 05, 2008 10:02 AM
To: r-help at r-project.org
Subject: [R] Running R Script on a Sequence of Files


I have about 900 files that I need to run the same R script on.  I  
looked over the R Data Import/Export Manual and  couldn't come up with  
a way to read in a sequence of files.

The files all have unique names and are in the same directory.  What I  
want to do is:
1) Create a list of the file names in the directory (this is really  
what I need help with)
2) For each item in the list...
	a) open the file with read.table
	b) perform some analysis
	c) append some results to an array or save them to another file
3) Next File

My initial instinct is to use Python to rename all the files with  
numbers 1:900 and then read them all, but the file names contain some  
information that I would like to keep intact and having to keep a  
separate database of original names and numbers seems inefficient.  Is  
there a way to have R read all the files in a directory one at a time?

- Chris

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