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="www.biomart.org", path="/biomart/martservice", port=80, archive=FALSE, local = FALSE, mysql = FALSE, user, password)

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).
host Host to connect to if different then www.biomart.org
path Path that should be pasted after to host to get access to the web service URL
port port to connect to, will be pasted between host and path
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
local MySQL access to Ensembl is no longer supported. biomaRt in web service mode supports all BioMart queries. Local BioMart databases can be accessed by specifying the local host which runs the local BioMart web service.
mysql MySQL access to Ensembl is no longer supported. biomaRt in web service mode supports all BioMart queries. Local BioMart databases can be accessed by specifying the local host which runs the local BioMart web service.
user MySQL access to Ensembl is no longer supported. biomaRt in web service mode supports all BioMart queries. Local BioMart databases can be accessed by specifying the local host which runs the local BioMart web service.
password MySQL access to Ensembl is no longer supported. biomaRt in web service mode supports all BioMart queries. Local BioMart databases can be accessed by specifying the local host which runs the local BioMart web service.

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 2.0.0 Index]