getGOTerm: Functions to Access GO data.

In Bioconductor/annotate: Annotation for microarrays

Functions to Access GO data.

Description

These functions provide access to data in the GO package. The data are assembled from publically available data from the Gene Ontology Consortium (GO), www.go.org. Given a list of GO identifiers they access the children (more specific terms), the parents (less specific terms) and the terms themselves.

Usage

getGOTerm(x)
getGOParents(x)
getGOChildren(x)
getGOOntology(x)

Arguments

x	A character vector of valid GO identifiers.

Details

GO consists of three (soon to be more) specific hierarchies: Molecular Function (MF), Biological Process (BP) and Cellular Component (CC). For more details consult the GO website. For each GO identifier each of these three hierarchies is searched and depending on the function called the appropriate values are obtained and returned.

It is possible for a GO identifier to have no children or for it to have no parents. However, it must have a term associated with it.

Value

A list of the same length as x. The list contains one entry for each element of x. That entry is itself a list. With one component named Ontology which has as its value one of MF, BP or CC. The second component has the same name as the suffix of the call, i.e. Children, Parents, or Term. If there was no match in any of the ontologies then a length zero list is returned for that element of x.

For getGOOntology a vector of categories (the names of which are the original GO term names). Elements of this list that are NA indicate term names for which there is no category (and hence they are not really term names).

Author(s)

R. Gentleman

References

The Gene Ontology Consortium

Examples

 library("GO.db")

 sG <- sample(keys(GO.db, "GOID"), 8)

 gT <- getGOTerm(sG)
 gP <- getGOParents(sG)
 gC <- getGOChildren(sG)
 gcat <- getGOOntology(sG)

Bioconductor/annotate documentation built on Nov. 2, 2024, 4:40 p.m.