listMarts: lists the available BioMart databases

Description Usage Arguments Details Author(s) Examples

View source: R/biomaRt.R

Description

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

Usage

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listMarts(mart = NULL, host="www.ensembl.org", path="/biomart/martservice",
port, includeHosts = FALSE, archive = FALSE, 
ensemblRedirect = NULL, 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

ensemblRedirect

This argument has now been deprecated.

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

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Example output



biomaRt documentation built on Nov. 8, 2020, 5:07 p.m.