hyperGTestCC: Hypergeometric testing with false discovery rate

In categoryCompare: Meta-analysis of high-throughput experiments using feature annotations

Description

Performs the hypergeometric testing for HyperGParamsCC objects.

Usage

hyperGTestCC(p)

Arguments

p	A HyperGParamsCC 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.

Value

Returns a HyperGResultCC object

Author(s)

Robert M Flight

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)

categoryCompare documentation built on Nov. 8, 2020, 5:59 p.m.