performGOEnrichment: Perform GO Enrichment

Description Usage Arguments Value Author(s) References Examples

View source: R/performGOEnrichment.R

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

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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

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data( goSTAG_example_gene_lists )
go_terms <- loadGOTerms()

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

goSTAG documentation built on May 2, 2018, 3:36 a.m.