listDatasets: List or search the datasets available in the selected BioMart...

Description Usage Arguments Author(s) Examples

View source: R/biomaRt.R

Description

Lists or search the datasets available in the selected BioMart database

Usage

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    listDatasets(mart, verbose = FALSE)
    searchDatasets(mart, pattern)

Arguments

mart

object of class Mart created with the useMart function

verbose

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

pattern

Character vector defining the regular expression (regex) to be used for the search. If left blank the default is to use ".*" which will match everything and return the same as listDatasets.

Author(s)

Steffen Durinck, Mike Smith

Examples

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if(interactive()){

    ## list the available Ensembl marts and use Ensembl Genes
    listEnsembl()
    ensembl <- useEnsembl(biomart = "ensembl")

    ## list the available datasets in this Mart
    listDatasets(mart = ensembl)

    ## the list of Ensembl datasets grows ever larger (101 as of Ensembl 93)
    ## we can search for a term of interest to reduce the length e.g. 'sapiens'
    searchDatasets(mart = ensembl, pattern = "sapiens")
    
    ## search for any dataset containing the word Rat or rat
    searchDatasets(mart = ensembl, pattern = "(R|r)at")
}

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