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 uselistMarts()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
TRUEwill 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 usinglistEnsemblArchives()- http_config
Some hosts require specific HTTP settings to be used when connecting. This argument takes the output of
httr::config()and will be used when connecting tohost. Can be ignored if you experience no problems accessinghost.- 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
maintenance' 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
Examples
if(interactive()){
listMarts()
}