useMart {biomaRt}R Documentation

Connects to the selected BioMart database and dataset

Description

A first step in using the biomaRt package is to select a BioMart database and dataset to use. The useMart function enables one to connect to a specified BioMart database and dataset within this database. To know which BioMart databases are available see the listMarts function. To know which datasets are available within a BioMart database, first select the BioMart database using useMart and then use the listDatasets function on the selected BioMart, see listDatasets function.

Usage

useMart(biomart, dataset, host, user, password, port, local = FALSE, mysql=FALSE, archive=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 use in MySQL connection
local boolean to specify if you want to use a locally installed BioMart or a mirror BioMart database
archive Boolean to indicate if you want to access archived versions od BioMart databases. This currently only works with mysql=TRUE and the ensembl BioMart database

Author(s)

Steffen Durinck,http://www.stat.berkeley.edu/~steffen

Examples

if(interactive()){

mart = useMart("ensembl")
mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")

}

[Package biomaRt version 1.16.0 Index]