Get GO gene sets — getBioMartGOGeneSets • BioMartGOGeneSets

Get GO gene sets

getBioMartGOGeneSets(dataset, ontology = "BP",
    as_table = FALSE, gene_id_type = "ensembl_gene")

Arguments

dataset: A BioMart dataset or a taxon ID. For a proper value, please see supportedOrganisms.
ontology: The value should be "BP", "CC", or "MF".
as_table: Whether to return the value as a data frame?
gene_id_type: Since BioMart is from Ensembl database, the default gene ID type is Ensembl gene ID. Depending on different organisms, Entrez ID ("entrez_gene") or gene symbol ("gene_symbol") can also be selected as the gene ID type.

Details

The gene sets are already compiled and are hosted on https://github.com/jokergoo/BioMartGOGeneSets_data , This function just simply retrieves data from there.

Value

A list of gene IDs or a data frame.

Examples

lt = getBioMartGOGeneSets("hsapiens_gene_ensembl")
lt = getBioMartGOGeneSets("hsapiens_gene_ensembl", gene_id_type = "entrez")
tb = getBioMartGOGeneSets("hsapiens_gene_ensembl", as_table = TRUE)