listEnsembl: lists the available BioMart databases hosted by Ensembl

Description Usage Arguments Author(s) Examples

View source: R/ensembl.R

Description

This function returns a list of BioMart databases hosted by Ensembl. To establish a connection use the useMart function.

Usage

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    listEnsembl(mart = NULL, host = "www.ensembl.org", version = NULL, 
                GRCh = NULL, mirror = NULL, verbose = FALSE)
    listEnsemblGenomes(includeHosts = FALSE)

Arguments

mart

mart object created with the useEnsembl function. This is optional, as you usually use listMarts to see which marts there are to connect to.

host

Host to connect to if different then 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.

verbose

Give detailed output of what the method is doing, for debugging purposes

includeHosts

If this option is set to TRUE a more detailed output is produced, including the URL used to access the corresponding mart.

Author(s)

Steffen Durinck, Mike L. Smith

Examples

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Example output



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