simplifyGOterms {compEpiTools} | R Documentation |
simplify a list of GeneOntology terms based on the list of genes assigned to each GO term
simplifyGOterms(goterms, maxOverlap= 0.8, ontology, go2allEGs)
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 |
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.
A subset of the (possibly unaltered) input goterms
http://genomics.iit.it/groups/computational-epigenomics.html
require(org.Mm.eg.db) simplifyGOterms(goterms=c('GO:0002320','GO:0002244'), maxOverlap= 0.1, ontology='BP', go2allEGs= org.Mm.egGO2ALLEGS)