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

In grimbough/biomaRt: Interface to BioMart databases (i.e. Ensembl)

Connects to the selected BioMart database and dataset hosted by Ensembl

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

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

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. For useEnsemblGenomes this argument can be used to specify an archive site.
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', '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

Details

The mirror argument can be considered as a "preferred choice" when connecting to Ensembl. If the argument is provided then connectivity to that mirror will be tested. If it responds positively then the requested mirror will be used. If the response is a failure each of the remaining mirrors will be selected at random and tested until a working server is found. Once identified that Ensembl server will be associated with the returned Mart object and will be used for all queries.

Author(s)

Steffen Durinck & Mike Smith

Examples

if(interactive()){

mart <- useEnsembl("ensembl")

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

## using the arabidopsis thaliana genes dataset in Ensembl Plants
plants_mart <- useEnsemblGenomes(biomart = "plants_mart",
                                 dataset = "athaliana_eg_gene")
                                 
## using the cucumis melo genes dataset in the Ensembl Plants 56 archive
plants_mart <- useEnsemblGenomes(biomart = "plants_mart",
                                 dataset = "cmelo_eg_gene",
                                 host = "https://eg56-plants.ensembl.org/")
}

grimbough/biomaRt documentation built on Aug. 7, 2024, 8:56 p.m.