Connects to the selected BioMart database and dataset

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 = "https://www.ensembl.org",
  path = "/biomart/martservice",
  port,
  version,
  verbose = FALSE
)

Arguments

biomart: BioMart database name you want to connect to. Possible database names can be retrieved with the function listMarts()
dataset: Dataset you want to use. To see the different datasets available within a biomaRt you can e.g. do: mart = useMart(), followed by listDatasets().
host: Host to connect to. Defaults to www.ensembl.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
version: Use version name instead of biomart name to specify which BioMart you want to use
verbose: Give detailed output of what the method is doing while in use, for debugging

Value

An object of class Mart, which can be used in functions such as getBM(), getLDS(), getGene(), etc. to retrieve data from the selected BioMart database.

Details

The previously available archive argument is defunct. 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 using listEnsemblArchives().

Author

Steffen Durinck, Mike L. Smith

Examples

if (FALSE) { # interactive()
mart <- useMart("ENSEMBL_MART_ENSEMBL")
mart <- useMart(
  biomart = "ENSEMBL_MART_ENSEMBL",
  dataset = "hsapiens_gene_ensembl"
)
}