humarray (version 1.2)

get.GO.for.genes: Retreive GO terms from biomart for a given gene list

Description

Gene-ontology terms (GO-terms) are commonly used for testing for simple functional enrichment for pathways, etc. This function can retrieve biological function, cellular component, or molecular description, depending on the parameters chosen.

Usage

get.GO.for.genes(gene.list, bio = T, cel = F, mol = F,
  host.txt = "may2009.archive.ensembl.org")

Arguments

gene.list

a list of gene, use HGNC names, like COMT, HLA-C, CTLA4, etc.

bio

logical, whether to return biological process GO terms

cel

logical, whether to return cellular component GO terms

mol

logical, whether to return molecular function GO terms

host.txt

character, the argument to pass to biomaRt::useMart(). Default is 'may2009.archive.ensembl.org', but more recently the recommended link is 'www.ensembl.org'

Value

data.frame containing the gene name in the first column, chromosome in the second column, and the GO terms in the third column, where one gene has multiple GO terms, this will produce multiple rows, so there will usually be more rows than genes entered. The data.frame can have 3,4 or 5 columns depending on how many GO terms are selected.

Examples

# NOT RUN {
get.GO.for.genes(c("CTLA4","PTPN2","PTPN22")) # biological terms (default)
get.GO.for.genes(c("CTLA4","PTPN2","PTPN22"),cel=TRUE) # add cellular GO terms
# }