biomartr (version 0.0.1)

getGO: Gene Ontology Query

Description

This function takes a gene id as character vector from a given query organism and returns the corresponding GO terms and additional GO information.

Usage

getGO(organism, genes, filters, database = "BioMart", email = NULL, ...)

Arguments

organism

a character string specifying the scientific name of a query organism.

genes

a character vector storing the gene ids of a organisms of interest to be queried against BioMart.

filters

a character vector specifying the filter (query key) for the BioMart query, e.g. filter = "ensembl_gene_id".

database

a cahracter string specifying the database from which GO information shall be retrieved. Possible choices are: database = "BioMart" and database = "DAVID".

email

a character string specifying the email address for your DAVID account. This parameter is only used to query DAVID web services and by default is email = NULL.

...

additional parameters that can be passed to the biomart function.

Details

This function takes the scientific name of a query organism, a set of genes for which GO terms and additional information shall be retrieved, and a filter argument that specifies the attribute for the query genes.

See Also

biomart, organismFilters, organismBM, getBM, getMarts, getDatasets, getFilters

Examples

GO_tbl <- getGO(organism = "Arabidopsis thaliana",
                genes    = c("AT1G06090", "AT1G06100",
                             "AT1G06110", "AT1G06120",
                             "AT1G06130", "AT1G06200"),
                filters  = "tair_locus")

# look at the result
head(GO_tbl[ , c("tair_locus","go_accession","go_name_1006")])