useEnsembl: Connects to the selected BioMart database and dataset hosted...

Description Usage Arguments Author(s) Examples

View source: R/ensembl.R

Description

A first step in using the biomaRt package is to select a BioMart database and dataset to use. The useEnsembl function enables one to connect to a specified BioMart database and dataset hosted by Ensembl without having to specify the Ensembl URL. To know which BioMart databases are available see the listEnsembl and listEnsemblGenomes functions. To know which datasets are available within a BioMart database, first select the BioMart database using useEnsembl and then use the listDatasets function on the selected Mart object.

Usage

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useEnsembl(biomart, dataset, host, version = NULL, 
            GRCh = NULL, mirror = NULL, verbose = FALSE)
useEnsemblGenomes(biomart, dataset)

Arguments

biomart

BioMart database name you want to connect to. Possible database names can be retrieved with the function listEnsembl

dataset

Dataset you want to use. To see the different datasets available within a biomaRt you can e.g. do: mart = useEnsembl('genes'), followed by listDatasets(mart).

host

Host to connect to. Only needs to be specified if different from www.ensembl.org

version

Ensembl version to connect to when wanting to connect to an archived Ensembl version

GRCh

GRCh version to connect to if not the current GRCh38, currently this can only be 37

mirror

Specify an Ensembl mirror to connect to. The valid options here are 'www', 'uswest', 'useast', 'asia'. If no mirror is specified the primary site at www.ensembl.org will be used. Mirrors are not available for the Ensembl Genomes databases.

verbose

Give detailed output of what the method is doing while in use, for debugging

Author(s)

Steffen Durinck & Mike Smith

Examples

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if(interactive()){

mart <- useEnsembl("ensembl")

## using the US West mirror
us_mart <- useEnsembl(biomart = "ensembl", mirror = "uswest")
}

biomaRt documentation built on Nov. 8, 2020, 5:07 p.m.