listFilters: List or search the filters available in the selected dataset

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

List or search the filters available in the selected dataset

Description

Filters are what we use as inputs for a biomaRt query. For example, if we want to retrieve all EntrezGene identifiers on chromosome X, chromosome will be the filter, with corresponding value X.

Usage

    listFilters(mart, what = c("name", "description"))
    searchFilters(mart, pattern)

Arguments

mart	object of class Mart created using the useMart function
what	character vector indicating what information to display about the available filters. Valid values are name, description, options, fullDescription, filters, type, operation, filters8, filters9.
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.

Author(s)

Steffen Durinck, Mike Smith

Examples

if(interactive()){

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

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

    ## the list of filters is long and not easy to read
    ## we can search for a term of interest to reduce this e.g. 'gene'
    searchFilters(mart = ensembl, pattern = "gene")
    
    ## search the available filters to find entries containing 'entrez' or 'hgnc'
    searchFilters(mart = ensembl, 'entrez|hgnc') 
}

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