connect_biomart: Connection to BioMart

In insightsengineering/hermes: Preprocessing, analyzing, and reporting of RNA-seq data

Connection to BioMart

Description

connect_biomart() creates a connection object of class ConnectionBiomart which contains the biomaRt object of class biomaRt::Mart and the prefix of the object which is used downstream for the query.

Usage

connect_biomart(prefix = c("ENSG", "GeneID"), version = NULL)

Arguments

prefix	(string) gene ID prefix.
version	(string or NULL) optional Ensembl version to use. If NULL the latest available release is used.

Details

This connects to the Ensembl data base of BioMart for human genes. A specific version can be optionally chosen to ensure reproducibility of results once a new release is available, as accessed data might then change.

Value

ConnectionBiomart object.

Examples

if (interactive()) {
  connection <- connect_biomart("ENSG")
}

insightsengineering/hermes documentation built on March 1, 2023, 5:58 a.m.