meshr (version 1.8.0)

meshHyperGTest: Hypergeometric Tests for MeSH term association

Description

Given a MeSHHyperGParams object containing a set of selected and background gene IDs, and gene-MeSH annotation data of interest, meshHyperGTest performs Hypergeomtric test for over-representation of each MeSH term accouting for the multiple testing correction.

Arguments

p

A MeSHHyperGParams object

Value

A MeSHHyperGResult object.

Details

For details on creating MeSHHyperGParams object, please read the documentation in the MeSHHyperGParams-class.

See Also

meshr-package, MeSHHyperGParams-class, MeSHHyperGResult-class

Examples

data(geneid.cummeRbund)
data(sig.geneid.cummeRbund)

meshParams <- new("MeSHHyperGParams", geneIds=sig.geneid.cummeRbund[,2], universeGeneIds=geneid.cummeRbund[,2], annotation="MeSH.Hsa.eg.db", category="Z", database="gene2pubmed", pvalueCutoff=0.05, pAdjust="none")

meshR <- meshHyperGTest(meshParams)