GOfuncR: Gene Ontology Enrichment Using FUNC

GOfuncR performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC. 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 Chi-square or Fisher's exact 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. 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, release 23-Mar-2020), is integrated in the package. It is also possible to provide custom gene coordinates, annotations and ontologies.

Installation

A stable release version can be obtained from Bioconductor.

• Installation from Bioconductor

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("GOfuncR")

The developmental (this) version can be obtained from the 'devel' version of Bioconductor or directly from GitHub:

• Installation from GitHub

if (!requireNamespace("devtools", quietly=TRUE))
    install.packages("devtools")
devtools::install_github("sgrote/GOfuncR")

Usage

See the vignette for an introduction.

Also refer to the man-pages for single functions, e.g.

library(GOfuncR)
?go_enrich
?get_anno_categories