jokergoo / BioMartGOGeneSets

Gene Ontology Gene Sets from BioMart

Gene Ontology Gene Sets from BioMart

The BioMartGOGeneSets contains pre-compiled GO gene sets for a huge number of organisms supported in BioMart. There are two types of data: 1. genes and 2 gene sets.

Install

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

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

Usage

To obtain the genes, use the function getBioMartGenes(). You need to provide a proper "dataset", which can be found with the function supportedOrganisms() (A complete list can be also found from https://jokergoo.github.io/BioMartGOGeneSets/articles/supported_organisms.html). Here we use the dataset "hsapiens_gene_ensembl" which is for human.

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

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

lt = getBioMartGOGeneSets("mmusculus_gene_ensembl")

The variable lt is a list of vectors where each vector corresponds to a GO gene set with Ensembl ID as gene identifiers.

In getBioMartGOGeneSets(), argument as_table can be set to TRUE, then the function returnes a data frame.

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

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

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

Last, argument gene_id_type can be set to "entrez_gene" or "gene_symbol", then genes in the gene sets are in Entrez IDs or gene symbols. Note this depends on specific organisms, that not every organism supports Entrez IDs or gene symbols.

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

To get the version of the data

The object BioMartGOGeneSets contains the version and source of data.

BioMartGOGeneSets

License

MIT @ Zuguang Gu