biomaRt: listMarts – R documentation

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listMarts

lists the available BioMart databases

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

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

if(interactive()){
listMarts()
}

biomaRt

Interface to BioMart databases (i.e. Ensembl)

v2.46.3

Artistic-2.0

Authors

Steffen Durinck [aut], Wolfgang Huber [aut], Sean Davis [ctb], Francois Pepin [ctb], Vince S Buffalo [ctb], Mike Smith [ctb, cre] (<https://orcid.org/0000-0002-7800-3848>)

Initial release