get.go.genesets {EnrichmentBrowser} | R Documentation |
This function retrieves GO gene sets for an organism under investigation either via download from BioMart or based on BioC annotation packages.
get.go.genesets( org, onto = c("BP", "MF", "CC"), mode = c("GO.db", "biomart"), cache = TRUE )
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'. |
cache |
Logical.
Should a locally cached version used if available?
Defaults to |
A list of gene sets (vectors of gene IDs).
Ludwig Geistlinger <Ludwig.Geistlinger@sph.cuny.edu>
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.
# 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")