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TheBioMartGOGeneSets contains pre-compiled GO gene sets for a huge number oforganisms supported inBioMart.There are two types of data: 1. genes and 2 gene sets.

If you want the latest version, install it directly from GitHub:

if (!requireNamespace("devtools",quietly=TRUE))    install.packages("devtools")devtools::install_github("jokergoo/BioMartGOGeneSets")

To obtain the genes, use the functiongetBioMartGenes(). You need to providea proper "dataset", which can be found with the functionsupportedOrganisms() (A complete list canbe also found fromhttps://jokergoo.github.io/BioMartGOGeneSets/articles/supported_organisms.html). Herewe use the dataset"hsapiens_gene_ensembl" which is for human.

library(BioMartGOGeneSets)gr= getBioMartGenes("hsapiens_gene_ensembl")

To obtain the gene sets, use the functiongetBioMartGOGeneSets(). Also you need to providethe "dataset". Here we use a different data"mmusculus_gene_ensembl".

lt= getBioMartGOGeneSets("mmusculus_gene_ensembl")

The variablelt is a list of vectors where each vector corresponds to a GO gene set with EnsemblID as gene identifiers.

IngetBioMartGOGeneSets(), argumentas_table can be set toTRUE, then the function returnesa data frame.

tb= getBioMartGOGeneSets("mmusculus_gene_ensembl",as_table=TRUE)

Argumentontology controls which category of GO gene sets. Possible values should be"BP","CC"and"MF".

getBioMartGOGeneSets("mmusculus_gene_ensembl",ontology="BP")# the default onegetBioMartGOGeneSets("mmusculus_gene_ensembl",ontology="CC")getBioMartGOGeneSets("mmusculus_gene_ensembl",ontology="MF")

Last, argumentgene_id_type can be set to"entrez_gene" or"gene_symbol", then genes in the gene setsare in Entrez IDs or gene symbols. Note this depends on specific organisms, that not every organism supportsEntrez IDs or gene symbols.

lt= getBioMartGOGeneSets("mmusculus_gene_ensembl",gene_id_type="entrez_gene")

To get the version of the data

The objectBioMartGOGeneSets contains the version and source of data.

BioMartGOGeneSets

MIT @ Zuguang Gu