listEnsembl: lists the available BioMart databases hosted by Ensembl

In grimbough/biomaRt: Interface to BioMart databases (i.e. Ensembl)

lists the available BioMart databases hosted by Ensembl

Description

This function returns a list of BioMart databases hosted by Ensembl. To establish a connection use the useEnsembl function.

Usage

    listEnsembl(mart = NULL, version = NULL, 
                GRCh = NULL, mirror = NULL, verbose = FALSE)
    listEnsemblGenomes(includeHosts = FALSE, host = NULL)

Arguments

mart	mart object created with the useEnsembl function. This is optional, as you usually use listMarts to see which marts there are to connect to.
version	Ensembl version to connect to when wanting to connect to an archived Ensembl version
GRCh	GRCh version to connect to if not the current GRCh38, currently this can only be 37
mirror	Specify an Ensembl mirror to connect to. The valid options here are 'www', 'useast', 'asia'. If no mirror is specified the primary site at www.ensembl.org will be used.
verbose	Give detailed output of what the method is doing, for debugging purposes
includeHosts	If this option is set to TRUE a more detailed output is produced, including the URL used to access the corresponding mart.
host	Host to connect to. Use this argument to specify and archive site for listEnsemblGenomes to work with.

Author(s)

Steffen Durinck, Mike L. Smith

Examples

if(interactive()){
listEnsembl()

## list the default Ensembl Genomes marts
listEnsemblGenomes()

## list only the marts available in the Ensmbl Plans 56 archive
listEnsemblGenomes(host = "https://eg56-plants.ensembl.org/")
}

grimbough/biomaRt documentation built on Aug. 7, 2024, 8:56 p.m.