R installation

This page describes how to install R for BioUML. You need to perform the following steps:

• R itself:

yum install R

or

apt-get install r-recommended

• Rserve:

apt-get install r-cran-rserve

• Set high enough socket connection timeout, add following line to /etc/R/Rprofile.site

options(timeout=864000L);

• BioConductor (from R-console):

source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite("makecdfenv", lib="/usr/local/lib/R/site-library")

• Illumina normalization (from R-console):

biocLite("lumi")

Note that this step may require installation of additional packages in the system like libxml2-dev, libglut3-dev, libcurl4-gnutls-dev.

• Agilent normalization (from R-console):

biocLite("limma")

• To use BioUML capabilities from R scripts install [RBioUML] package:

install.packages("rbiouml")

See also

• Using R in BioUML