limma (version 3.22.7)

goana: Gene Ontology Analysis

Description

Test for over-representation of gene ontology (GO) terms in one or more sets of genes.

Usage

"goana"(de, universe = NULL, species = "Hs", prior.prob = NULL, ...)

Arguments

de

a vector of Entrez Gene IDs, or a list of such vectors.

universe

vector specifying the set of Entrez Gene identifiers to be the background universe. If NULL then all Entrez Gene IDs associated with any gene ontology term will be used as the universe.

species

species identifier. Possible values are "Hs", "Mm", "Rn" or "Dm".

prior.prob

numeric vector giving the prior probability that each gene in the universe appears in a gene set.

...

other arguments are not currently used.

Value

A data frame with a row for each GO term and the following columns:

Term

GO term.

Ont

ontology that the GO term belongs to. Possible values are "BP", "CC" and "MF".

N

number of genes in the GO term.

DE1

number of genes in the DE1 set.

P.DE1

p-value for over-representation of the GO term in the set.

The last two column names above assume one gene set with the name DE1. In general, there will be a pair of such columns for each gene set and the name of the set will appear in place of "DE1".The row names of the data frame give the GO term IDs.

Details

goana is an S3 generic function. The default method performs a Gene Ontology enrichment analysis for one for more gene lists using the appropriate Bioconductor organism package. The gene lists must be supplied as Entrez Gene IDs.

If prior.prob=NULL, the function computes one-sided hypergeometric tests equivalent to Fisher's exact test.

The prior.prob vector can be used to specify the prior probability that each gene in the universe appears in a gene set. If prior probabilities are specified, then a test based on the Wallenius' noncentral hypergeometric distribution is used to adjust for the relative probability that each gene will appear in a gene set, following the approach of Young et al (2010).

References

Young, M. D., Wakefield, M. J., Smyth, G. K., Oshlack, A. (2010). Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biology 11, R14. http://genomebiology.com/2010/11/2/R14

See Also

goana.MArrayLM, topGO

The goseq package implements a similar GO analysis. The goseq version will work with a variety of gene identifiers, not only Entrez Gene as here, and includes a database of gene length information for various species.

The gostats package also does GO analyses with some different options.

Examples

## Not run: 
# 
# go.de <- goana(list(DE1 = EG.DE1, DE2 = EG.DE2, DE3 = EG.DE3))
# topGO(go.de, sort = "DE1")
# topGO(go.de, sort = "DE2")
# topGO(go.de, ontology = "BP", sort = "DE3")
# topGO(go.de, ontology = "CC", sort = "DE3")
# topGO(go.de, ontology = "MF", sort = "DE3")
# ## End(Not run)