useMart {biomaRt}R Documentation

Connects to the selected BioMart

Description

This function connects to the selected BioMart

Usage

useMart(biomart, dataset, host, user, password, port, local = FALSE, mysql=FALSE)

Arguments

biomart BioMart database name you want to connect to. Possible database names can be retrieved with the functio listMarts
dataset Dataset you want to use. To see the different datasets available within a biomaRt you can e.g. do: mart = useMart('ensembl'), followed by listDatasets(mart).
mysql Boolean to specify if you want to access BioMart database via MySQL or via it's webservice of HTTP. Default is using the webservice.
host If you want to use a local host or a miror database, use vector of hosts. For connecting to public BioMarts this parameter is not required
user username, use vector of usernames for non public or miror BioMarts
password password, use vector of passwords for non-public or miror BioMarts
port port to connect to via MySQL
local boolean to specify if you want to use a locally installed BioMart or a mirror BioMart database

Author(s)

Steffen Durinck, http://www.esat.kuleuven.ac.be/~sdurinck

Examples

if(interactive()){

mart = useMart("ensembl")

#if the dataset you wish to use is known you can do:
mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")

}

[Package biomaRt version 1.8.2 Index]