annFUN {topGO}R Documentation

functions to map gene IDs to GO terms

Description

These functions are used to compile a list of GO terms and their mappings to gene identifiers.

Usage

annFUN.hgu(whichOnto, feasibleGenes = NULL, affyLib)
annFUN.gene2GO(whichOnto, feasibleGenes = NULL, gene2GO)
annFUN.GO2genes(whichOnto, feasibleGenes = NULL, GO2genes)

Arguments

whichOnto character string specifying one of the three GO ontologies: "BP", "MF", "CC"
feasibleGenes character vector containing a subset of gene identifiers. Only these genes will be used to annotate GO terms. Default value is NULL which means all gene identifiers will be used.
affyLib character string containing the name of the Affymetrix chip.
gene2GO named list of character vectors. The list names are genes identifiers. For each gene the character vector contains the GO terms IDs it maps to. Only the most specific annotations are required.
GO2genes named list of character vectors. The list names are GO terms IDs. For each GO the character vector contains the genes identifiers which are mapped to it. Only the most specific annotations are required.

Details

The function annFUN.hgu should be used when the gene identifiers are Affymetrix IDs. It uses the mappings provided in the Bioconductor annotation data packages. For example, if the Affymetrix hgu133a chip it is used, then the user should set affyLib = "hgu133a".

The functions annFUN.gene2GO and annFUN.GO2genes are used when the user provide his own annotations.

All these function restrict the GO terms to the ones belonging to the specified ontology.

Value

A named(GO terms IDs) list of character vectors.

Author(s)

Adrian Alexa

See Also

topGOdata-class

Examples


library(hgu133a)
set.seed(111)

## generate a gene list and the GO annotations
numGenes <- 50
selGenes <- sample(ls(hgu133aGO), numGenes)
gene2GO <- lapply(mget(selGenes, envir = hgu133aGO), names)
gene2GO[sapply(gene2GO, is.null)] <- NA

## the annotation for the first three genes
gene2GO[1:3]

## inverting the annotations
go2genes <- annFUN.gene2GO(whichOnto = "CC", gene2GO = gene2GO)


## generate a GO list with the genes annotations
numGO <- 30
selGO <- sample(ls(hgu133aGO2PROBE), numGO)
GO2gene <- lapply(mget(selGO, envir = hgu133aGO2PROBE), as.character)

GO2gene[1:3]

## select only the GO terms for a specific ontology
go2gene <- annFUN.GO2genes(whichOnto = "CC", GO2gene = GO2gene)


[Package topGO version 1.2.1 Index]