simplifyGOterms {compEpiTools} | R Documentation

## 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

### 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)

[Package compEpiTools version 1.21.1 Index]