categoryCompare (version 1.16.2)

hyperGTestCC: Hypergeometric testing with false discovery rate

Description

Performs the hypergeometric testing for HyperGParamsCC objects.

Usage

hyperGTestCC(p)

Arguments

p

A HyperGParamsCC object

Value

HyperGResultCC object

Details

This is the heart of categoryCompare, the function that calculates the HyperGeometric statistics for the given categories of annotation for each gene list.

See Also

HyperGParamsCC HyperGResultCC GOHyperGParamsCC KEGGHyperGParamsCC GOHyperGResultCC KEGGHyperGResultCC

Examples

require(GO.db)
require(org.Hs.eg.db)
data(ccData)
g10 <- unique(table10$Entrez)
testGO <- new("GOHyperGParamsCC", geneIds=g10, universeGeneIds=gUniverse, 
annotation="org.Hs.eg.db", ontology="CC", conditional=FALSE, 
testDirection="over",fdr=0, pvalueCutoff = 0.01)
# ccHypRes <- hyperGTestCC(testGO)
# summary(ccHypRes)