Description Usage Arguments Details Author(s) Examples
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.
1 2 3 |
mart |
mart object created with the |
host |
Host to connect to. Defaults to |
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 |
ensemblRedirect |
This argument has now been deprecated. |
verbose |
Give detailed output of what the method is doing, for debugging purposes |
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
Steffen Durinck, Mike Smith
1 2 3 | if(interactive()){
listMarts()
}
|
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