compEpiTools (version 1.6.3)

simplifyGOterms: simplify a list of GO terms

Description

simplify a list of GeneOntology terms based on the list of genes assigned to each GO term

Usage

simplifyGOterms(goterms, maxOverlap= 0.8, ontology, go2allEGs)

Arguments

goterms

character; a vector of GO ids

maxOverlap

numeric in (0,1) see details

ontology

character; one of BP, MF or CC

go2allEGs

the species specific assignment of each GO term to EntrezGene ids

Value

Details

Given a pair of parent and child GO terms, and the Entrez Gene ids (genes sets) which can be assigned to them, the parent GO term is defined as redundant if the two gene sets overlap more than 100*maxOverlap percent of the parent genes. Given a set goterms, this rule is applied to discard redundant parent terms while keeping the corresponding children terms.

References

http://genomics.iit.it/groups/computational-epigenomics.html

Examples

require(org.Mm.eg.db)
simplifyGOterms(goterms=c('GO:0002320','GO:0002244'), maxOverlap= 0.1, ontology='BP', go2allEGs= org.Mm.egGO2ALLEGS)