useMart

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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.

Keywords
methods
Usage
useMart(biomart, dataset, host="www.ensembl.org", path="/biomart/martservice", port=80, archive=FALSE, ssl.verifypeer = TRUE, version, verbose = FALSE)
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 of BioMart databases. Note that this gives access to only a limited number of archived BioMarts and the most recent archives are often not available. A better alternative is to leave archive = FALSE and to specify the url of the archived BioMart you want to access see vignette for an example.
ssl.verifypeer
Set SSL peer verification on or off. By default ssl.verifypeer is set to TRUE
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
Aliases
  • useMart
Examples
if(interactive()){

mart = useMart("ensembl")
mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
}
Documentation reproduced from package biomaRt, version 2.28.0, License: Artistic-2.0

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