List or search the filters available in the selected dataset

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

Steffen Durinck, Mike Smith

Examples

if (FALSE) { # interactive()
## list the available Ensembl marts and use Ensembl Genes
listEnsembl()
ensembl <- useEnsembl(
  biomart = "ENSEMBL_MART_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')
}