Gene Set Enrichment Analysis in R

R CMD build GSEAlite

R CMD install GSEAlite_1.0.tar.gz

library(GSEAlite)

Follow the example in GSEA.listofgenes

?GSEA.listofgenes

To read in GMT files from the MSigDB

?readgmt

Follow the example in GSEAplot

?GSEAplot

You can use any scoring function to use within GSEA for the enrichment.

Two such functions are already coded within the R package environment: snr.SNR and snr.FC, for the t-test-like signal-to-noise ratio and the fold-change, repsectively.

To use a new scoring function, define a new function in the global environment with its name following the syntax:

snr.NAMEOFSCORINGFUNCTION = function(m, o)

For example you could redefine a function that is a median fold-change:

snr.MedianFC = function( m, o) apply(m,1,function(x) median(x[o==levels(o)[1]]) -median(x[o==levels(o)[2]]))

GSEA can then be run using snr.MedianFC as scoring function, by specifying as input parameters:

metric = "MedianFC"