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
Examples
if(interactive()){
mart = useMart("ensembl")
mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
}