goEnrichTest: Computes a Gene Ontology (GO) enrichment test using the...

In asishallab/GeneFamilies: Analyses different properties of gene families

Computes a Gene Ontology (GO) enrichment test using the functions from #' package GOstats and GSEABase.

Description

Computes a Gene Ontology (GO) enrichment test using the functions from #' package GOstats and GSEABase.

Usage

goEnrichTest(gsc, gene.ids, univ.gene.ids, ontologies = c("BP", "CC",
  "MF"), pvalue.cutoff = 0.01, cond = FALSE, test.dir = "over",
  p.adjust.method = "fdr")

Arguments

gsc	An instance of gene set collection [package GEABase]
gene.ids	A character vector of gene IDs among which to look for enriched GO terms
univ.gene.ids	A character vector of 'background' gene IDs to be used as reference GO annotations when looking for overrepresentations in 'gene.ids'
ontologies	A character vector of the Gene Ontology categories to compute enrichment tests for, default is 'BP', 'CC', and 'MF'
pvalue.cutoff	The significance level, default to 0.01
cond	If set to TRUE already found to be enriched GO annotations wont be counted when testing enrichment for parental terms, default is FALSE
test.dir	Set to 'over' to infer overrepresentation, set to 'under' if the opposite is wanted.
p.adjust.method	The method used to adjust p-values for multiple hypothesis testing, default is 'fdr'. See function p.adjust for details.

Value

A named list with enriched GO terms in the argument GO categories.

asishallab/GeneFamilies documentation built on July 28, 2024, 11:44 a.m.