get_ontology: Run GO enrichment analysis for a specified ontology.

In vitalinakomashko/parallelGO: Parallel Implementation for Extraction of GO Results

Description

get_ontology uses hyperGTest to calculate hypergeometric statistics (for over-representation of each GO term); GOstats::summary to return the summarized results with adjusted p values using p.adjust function and the method "bonferroni".

Usage

get_ontology(gene_id, universe, annotation, ontology, set_label)

Arguments

gene_id	Character vector of unique ENTREZ gene identifiers of interest.
universe	Character vector of unique ENTREZ gene identifiers to be used as a universe.
annotation	Character string with the name of the annotation data package.
ontology	Character string specifying the ontology, must be either "BP", "CC" or "MF".
set_label	Character string used to populate the column set_label. This parameter is optional. It is used for identification of results when get_ontology is used in a loop.

Value

Data frame with the following columns: goid, pvalue, odds_ratio, exp_count, count, size, term, p_bonferroni, ontology, set_label (if provided).

See Also

hyperGTest, GOstats::summary.

vitalinakomashko/parallelGO documentation built on May 18, 2019, 1:32 p.m.