useMart {biomaRt} | R Documentation |
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.
useMart(biomart, dataset, host, user, password, port, local = FALSE, mysql=FALSE, archive=FALSE)
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 |
Steffen Durinck,http://www.stat.berkeley.edu/~steffen
if(interactive()){ mart = useMart("ensembl") mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl") }