hyperGTest: Hypergeometric Tests for GO term association

In Bioconductor/GOstats: Tools for manipulating GO and microarrays

Hypergeometric Tests for GO term association

Description

Given a GOHyperGParams instance containing a set of unique Entrez Gene Identifiers, a microarray annotation data package name, and the GO ontology of interest, this function will compute Hypergeomtric p-values for over or under-representation of each GO term in the specified ontology among the GO annotations for the interesting genes. The computations can be done conditionally based on the structure of the GO graph.

Arguments

p	A GOHyperGParams or OBOHyperGParams instance

Details

When conditional(p) == TRUE, the hyperGTest function uses the structure of the GO graph to estimate for each term whether or not there is evidence beyond that which is provided by the term's children to call the term in question statistically overrepresented.

The algorithm conditions on all child terms that are themselves significant at the specified p-value, odds ratio, minimum or maximum gene set size cutoff. Given a subgraph of one of the three GO ontologies, or the ontology given in the OBOHyperGParams instance, the terms with no child categories are tested first. Next the nodes whose children have already been tested are tested. If any of a given node's children tested significant, the appropriate conditioning is performed.

Value

A GOHyperGResult or OBOHyperGResult instance.

Author(s)

Seth Falcon

References

FIXME

See Also

GOHyperGResult-class, geneGoHyperGeoTest, geneKeggHyperGeoTest

Bioconductor/GOstats documentation built on Oct. 29, 2023, 4:17 p.m.