GO_similarity: Calculate Gene Ontology (GO) semantic similarity matrix

In jokergoo/simplifyGO: Simplify Functional Enrichment Results

Calculate Gene Ontology (GO) semantic similarity matrix

Description

Calculate Gene Ontology (GO) semantic similarity matrix

Usage

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

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. The value can also directly be a OrgDb object.
measure	Semantic measure for the GO similarity, pass to termSim.
remove_orphan_terms	Whether to remove terms that have zero similarity to all other terms?

Details

This function is basically a wrapper on termSim.

Value

A symmetric matrix.

Examples

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

jokergoo/simplifyGO documentation built on Oct. 25, 2023, 9:02 p.m.