genesInEnrichedCategories: Function to intersect a gene list with enriched categories

In uc-bd2k/CLEAN: Clustering Enrichment Analysis

Function to intersect a gene list with enriched categories

Description

This function takes a gene list and a list of IDs of (enriched) categories and returns a bolean matrix where each column indicates whether or not the gene is member of the corresponding categories.

Usage

genesInEnrichedCategories(categoryIDs, geneList, funcCategories = NULL, species = NULL)

Arguments

categoryIDs	A list of functional category IDs.
geneList	A gene list to be tested for enrichment of functional categories.
funcCategories	A collection of gene sets, representing functional categories.
species	Two letter description of the species to be used to generate gene ontology categories (e.g. "Hs" for human, "Mm" for mouse). This parameter is used when funcCategories = "GO"

Details

coming soon.

Value

A matrix with rows representing the functional categories and columns representing the genes.

Author(s)

Johannes Freudenberg, Xiangdong Liu, Mario Medvedovic.

References

Coming soon.

See Also

geneListEnrichment

Examples

data(gimmOut)
require(CLEAN.Rn)
require(org.Rn.eg.db)

geneList <- gimmOut$clustData[,1]
allGenes <- unique(keys(org.Rn.egSYMBOL)) #one should really use the list of
                                          #genes represented on the microarray instead
res <- geneListEnrichment(geneList, allGenes, functionalCategories = "GO",
	species = "Rn", sigFDR = 0.01, maxGenesInCategory = 10000)

#display membership of each gene in top ten categories
genesInEnrichedCategories(res[1:10,1], geneList, funcCategories = "GO", species = "Rn")

uc-bd2k/CLEAN documentation built on Sept. 22, 2022, 4:12 a.m.