listMarts: lists the available BioMart databases

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

lists the available BioMart databases

Description

This function returns a list of BioMart databases to which biomaRt can connect. By default the Ensembl BioMart databases are displayed. To establish a connection use the useMart function.

Usage

listMarts(mart = NULL, host="https://www.ensembl.org", path="/biomart/martservice",
port, includeHosts = FALSE, archive = FALSE, http_config, verbose = FALSE)

Arguments

mart	mart object created with the useMart function. This is optional, as you usually use listMarts to see which marts there are to connect to.
host	Host to connect to. Defaults to www.ensembl.org
path	path to martservice that should be pasted behind the host to get to web service URL
port	port to use in HTTP communication
includeHosts	boolean to indicate if function should return host of the BioMart databases
archive	Boolean to indicate if you want to access archived versions of BioMart database. Note that this argument is now defunct and setting this value to TRUE will produce an error. A better alternative is to specify the url of the archived BioMart you want to access. For Ensembl you can view the list of archives using listEnsemblArchives
http_config	Some hosts require specific HTTP settings to be used when connecting. This argument takes the output of config and will be used when connecting to host. Can be ignored if you experience no problems accessing host.
verbose	Give detailed output of what the method is doing, for debugging purposes.

Details

If you receive an error message saying 'Unexpected format to the list of available marts', this is often because there is a problem with the BioMart server you are trying to connect to, and something other than the list of available marts is being returned - often some like a 'down for maintainance' page. If you browse to the provided URL and find a page that starts with '<MartRegistry>' this is the correct listing and you should report the issue on the Bioconductor support site: https://support.bioconductor.org

Author(s)

Steffen Durinck, Mike Smith

Examples

if(interactive()){
listMarts()
}

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