performGOEnrichment: Perform GO Enrichment

In brianbennettphd/goSTAG: A tool to use GO Subtrees to Tag and Annotate Genes within a set

Description

Performs a GO enrichment analysis on a set of gene lists and GO terms. Will filter out GO terms having no significant enrichment in any of the gene lists.

Usage

performGOEnrichment(gene_lists, go_terms, filter_method = "pval", significance_threshold = 0.05, p.adjust_method = "BH")

Arguments

gene_lists	A list of vectors. Each element of the list corresponds to a gene list, and each vector contains the genes in the gene list.
go_terms	A list of vectors. Each element of the list corresponds to a GO term, and each vector contains the genes associated with the GO term. The list must also have an additional element named "ALL", which is a vector that contains all annotated genes.
filter_method	A value indicating whether to filter out GO terms based on a nominal p-value or an adjusted p-value. Acceptable options are "pval" (nominal p-value) or "p.adjust" (adjusted p-value).
significance_threshold	The significance threshold at which to filter out GO terms. GO terms with a nominal or adjusted p-value (indicated by "filter_method") of greater than or equal to this threshold in all gene lists will be filtered out.
p.adjust_method	The correction method used to adjust the p-values. Available options are those of the "method" argument for the "p.adjust" function, which are currently "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", or "none". Only applicable when filter_method = "p.adjust".

Value

A matrix of enrichment scores. Rows correspond to GO terms and columns correspond to gene lists.

Author(s)

Brian D. Bennett
Pierre R. Bushel

References

Bennett BD and Bushel PR. goSTAG: Gene Ontology Subtrees to Tag and Annotate Genes within a set. Source Code Biol Med. 2017 Apr 13.

Examples

data( goSTAG_example_gene_lists )
go_terms <- loadGOTerms()

enrichment_matrix <- performGOEnrichment( goSTAG_example_gene_lists, go_terms )
head( enrichment_matrix )

brianbennettphd/goSTAG documentation built on Nov. 14, 2020, 7:21 a.m.