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,
  archive = FALSE,
  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
archive: Boolean to indicate if you want to access archived versions of BioMart databases. Note that this argument is now deprecated and will be removed in the future. A better alternative is to leave archive = FALSE and to specify the url of the archived BioMart you want to access. For Ensembl you can view the list of archives using listEnsemblArchives()
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

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"
)
}