EnrichmentBrowser (version 2.2.2)

get.go.genesets: Definition of gene sets according to the Gene Ontology (GO)

Description

This function retrieves GO gene sets for an organism under investigation either via download from BioMart or based on BioC annotation packages.

Usage

get.go.genesets( org, onto = c("BP", "MF", "CC"), mode = c("GO.db","biomart") )

Arguments

org

An organism in (KEGG) three letter code, e.g. ‘hsa’ for ‘Homo sapiens’.

onto

Character. Specifies one of the three GO ontologies: 'BP' (biological process), 'MF' (molecular function), 'CC' (cellular component). Defaults to 'BP'.

mode

Character. Determines in which way the gene sets are retrieved. This can be either 'GO.db' or 'biomart'. The 'GO.db' mode creates the gene sets based on BioC annotation packages - which is fast, but represents not necessarily the most up-to-date mapping. In addition, this option is only available for the currently supported model organisms in BioC. The 'biomart' mode downloads the mapping from BioMart - which can be time consuming, but allows to select from a larger range of organisms and contains the latest mappings. Defaults to 'GO.db'.

Value

A list of gene sets (vectors of gene IDs).

References

http://geneontology.org/

See Also

annFUN for general GO2gene mapping used in the 'GO.db' mode, the biomaRt package for general queries to BioMart, get.kegg.genesets for defining gene sets according to KEGG, parse.genesets.from.GMT to parse user-def. gene sets from file.

Examples

    # Typical usage for gene set enrichment analysis:
    # Biological process terms based on BioC annotation (for human)
    gs <- get.go.genesets("hsa")
    
    # eq.:  
    # gs <- get.go.genesets(org="hsa", onto="BP", mode="GO.db")

    # Alternatively:
    # downloading from BioMart 
    # this may take a few minutes ...
    
    gs <- get.go.genesets(org="hsa", mode="biomart")