BicARE (version 1.30.0)

testSet: Find gene sets that are enriched in a bicluster

Description

Test of the over-representation of gene sets in the biclusters

Usage

testSet(resBic, geneSetCol)

Arguments

resBic

a biclustering object created by FLOC

geneSetCol

a GeneSetCollection-class

Value

A biclustering object containing resBic and updated with the results of the tests in resBic$geneSet.The results are presented as a list with :

GeneSetCollection

the GeneSetCollection used

pvalues

a matrix containing the pvalues of the tests for each geneSet and each bicluster

adjpvalue

a matrix containing the p-values adjusted by the Benjamini Yekutieli procedure

Details

The over-representation of a gene set in a bicluster is evaluated by an hypergeometric test. The genes identifiers of the gene sets will automatically be mapped to the same as those used in the data. Due to the amount of results it is advised to use the makeReport function to get a html report.

Examples

data(sample.biclustering)
gss <- GeneSetCollection(sample.biclustering$ExpressionSet[1:50,], setType=GOCollection())
resBic <- testSet(sample.biclustering, gss)