RSPerl : Using R from within Perl

October 23, 2009

(This article was first published on compBiomeBlog, and kindly contributed to R-bloggers)

Some things I write in perl some in R, sometime I use perl to write R and run R. One thing that I find very useful is the functionality of RSPerl which enables you to call R functions from within perl and on perl variables. It can also call perl from R, though I have no idea why you would want to do this.

My main use is to carry out statistical tests on the results of things carried out in. For example I use perl to run patser to count the number of hits to a position weight matrix in a test sequence and a background sequences, then I use RSPerl to calculate the p-value via the binomial test (binom.test function).

It was a pain to setup, as I had to recompile R and install various modules in the correct places and setup some environment variables. Once working though it is a great tool. You can even use R’s great graphical capabilities to automatically generate figures from data in perl variables.

perl -e ‘use R;&R::initR(“–silent”,”–vanilla”);&R::eval(“r <- rnorm(100);plot(r,pch=20)");'

This one plots a histogram of the length of perl scripts!

for f in *.pl; do wc -l ${f}|cut -f 1 -d ” “; done | perl -ne ‘s/\n/,/g;print;’ |perl -ne ‘use R;&R::initR(“–silent”,”–vanilla”);chop;&R::eval(“hist(c($_),main=\”File Lengths\”,xlab=\”Number of Lines\”)”);sleep 10’


To leave a comment for the author, please follow the link and comment on their blog: compBiomeBlog. offers daily e-mail updates about R news and tutorials on topics such as: Data science, Big Data, R jobs, visualization (ggplot2, Boxplots, maps, animation), programming (RStudio, Sweave, LaTeX, SQL, Eclipse, git, hadoop, Web Scraping) statistics (regression, PCA, time series, trading) and more...

If you got this far, why not subscribe for updates from the site? Choose your flavor: e-mail, twitter, RSS, or facebook...

Comments are closed.

Search R-bloggers


Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)

Click here to close (This popup will not appear again)