simplifyGOterms: simplify a list of GO terms

In kamalfartiyal84/compEpiTools: Tools for computational epigenomics

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

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.

Value

A subset of the (possibly unaltered) input goterms

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)

kamalfartiyal84/compEpiTools documentation built on May 29, 2019, 5:40 a.m.