This page contains the R package IndirectEffects, implementing the methodology described in the following paper:
Egil Ferkingstad, Arnoldo Frigessi and Heidi Lyng (2008), Indirect genomic effects on survival from gene expression data. Genome Biology, 9(3) R58.
Prerequisites:
To use this package, the packages ggm and igraph need to be installed first. Install these using the command
install.packages(c("ggm","igraph"))
Installation:
Windows:
Download IndirectEffects_1.0.zip.
In R, choose "Install package(s) from local zip files..." from the "Packages" menu. Choose the zip file you just downloaded.
Unix (including MacOS and Linux):
Download the source package IndirectEffects_1.0.tar.gz to your R working directory. Install the package by typing
install.packages("IndirectEffects_1.0.tar.gz",repos=NULL,type="source")
Usage:
library(IndirectEffects)
?IndirectEffects
loads the package into R and displays the documentation. Example data and code is included.
In case you want to look at the documentation without installing the package, it's available in PDF format here.
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Egil Ferkingstad
egil(at)nr.no