View source: R/enrichment_funks.R
goEnrichTest | R Documentation |
Computes a Gene Ontology (GO) enrichment test using the functions from #' package GOstats and GSEABase.
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")
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. |
A named list with enriched GO terms in the argument GO categories.
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