getGO: Gene Ontology Query

Description Usage Arguments Details Author(s) See Also Examples

View source: R/getGO.R

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

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getGO(organism, genes, filters, ...)

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 Ensembl Biomart.

filters

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

...

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.

Author(s)

Hajk-Georg Drost

See Also

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

Examples

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## Not run:  
GO_tbl <- getGO(organism = "Arabidopsis thaliana", 
                genes    = c("AT1G06090", "AT1G06100"),
                filters  = "ensembl_gene_id")

# look at the result
head(GO_tbl)

## End(Not run)

biomartr documentation built on July 2, 2018, 1:02 a.m.