GO_similarity: Calculate Gene Ontology (GO) semantic similarity matrix

In simplifyEnrichment: Simplify Functional Enrichment Results

Description

Calculate Gene Ontology (GO) semantic similarity matrix

Usage

GO_similarity(go_id, ont, db = 'org.Hs.eg.db', measure = "Rel")

Arguments

go_id	A vector of GO IDs.
ont	GO ontology. Value should be one of "BP", "CC" or "MF". If it is not specified, the function automatically identifies it by random sampling 10 IDs from go_id (see guess_ont).
db	Annotation database. It should be from https://bioconductor.org/packages/3.10/BiocViews.html#___OrgDb
measure	Semantic measurement for the GO similarity, pass to termSim.

Details

This function is basically a wrapper on termSim.

Value

A symmetric matrix.

Examples

go_id = random_GO(100)
mat = GO_similarity(go_id)

simplifyEnrichment documentation built on Nov. 8, 2020, 5:07 p.m.