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

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

List or search the datasets available in the selected BioMart database

Description

Lists or search the datasets available in the selected BioMart database

Usage

    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

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")
}

grimbough/biomaRt documentation built on Feb. 11, 2024, 8:20 p.m.