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.db(whichOnto, feasibleGenes = NULL, affyLib)
    annFUN(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.db` 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.db"`.

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.db)
    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 1.8.1 Index]