1 Overview

GOfuncR performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC [1,2]. It provides the standard candidate vs. background enrichment analysis using the hypergeometric test, as well as three additional tests: (i) the Wilcoxon rank-sum test that is used when genes are ranked, (ii) a binomial test that can be used when genes are associated with two counts, e.g. amino acid changes since a common ancestor in two different species, and (iii) a 2x2 contingency table test that is used in cases when genes are associated with four counts, e.g. non-synonymous or synonymous variants that are fixed between or variable within species.
To correct for multiple testing and interdependency of the tests, family-wise error rates (FWER) are computed based on random permutations of the gene-associated variables (see Schematic 1 below). GOfuncR also provides tools for exploring the ontology graph and the annotations, and options to take gene-length or spatial clustering of genes into account during testing.
GO-annotations and gene-coordinates are obtained from OrganismDb packages (Homo.sapiens by default) or OrgDb and TxDb packages. The gene ontology graph (obtained from geneontology, last modified on 11-Oct-2018), is integrated in the package. It is also possible to provide custom gene coordinates, annotations and ontologies.