List or search the options available for a specified filter.

Some filters have a predefined list of values that can be used to search them. These functions give access to this list of options for a named filter, so you can check in the case where your biomaRt query is not finding anything.

Usage

searchFilterOptions(mart, filter, pattern = ".*")

listFilterOptions(mart, filter)

Arguments

mart

object of class Mart created using the useMart(), or useEnsembl() functions

filter

The name of the filter whose options should be listed or searched. You can list available filters via listFilters()

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.

See also

listFilters()

Author

Mike Smith

Examples

if (FALSE) { # interactive()
## Use the Ensembl human genes dataset
ensembl <- useEnsembl(
  biomart = "ENSEMBL_MART_ENSEMBL",
  dataset = "hsapiens_gene_ensembl"
)

## we can search for the name of a filter we're interested in e.g. 'phenotype'
## we need to use the name of the filter in the next function
searchFilters(ensembl, pattern = "phenotype")

## list all the options available to the 'phenotype_source' filter
listFilterOptions(mart = ensembl, filter = "phenotype_source")

## search the 'phenotype_description' filter for the term 'crohn'
searchFilterOptions(
  mart = ensembl,
  filter = "phenotype_description",
  pattern = "crohn"
)
}