biomaRt: useMart – R documentation

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useMart

Connects to the selected BioMart database and dataset

Description

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, ensemblRedirect = NULL, 
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. 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`
`ensemblRedirect`	This argument has now been deprecated.
`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(s)

Steffen Durinck

Examples

if(interactive()){

mart = useMart("ensembl")
mart=useMart(biomart="ensembl", dataset="hsapiens_gene_ensembl")
}

biomaRt

Interface to BioMart databases (i.e. Ensembl)

v2.46.3

Artistic-2.0

Authors

Steffen Durinck [aut], Wolfgang Huber [aut], Sean Davis [ctb], Francois Pepin [ctb], Vince S Buffalo [ctb], Mike Smith [ctb, cre] (<https://orcid.org/0000-0002-7800-3848>)

Initial release