listFilterValues: List or search the options available for a specified filter.
In biomaRt: Interface to BioMart databases (i.e. Ensembl)

Description Usage Arguments Author(s) See Also Examples

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.

1 2	listFilterValues(mart, filter) searchFilterValues(mart, filter, pattern)

`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.

Mike Smith

listFilters

if(interactive()){

    ## Use the Ensembl human genes dataset
    ensembl <- useEnsembl(biomart = "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
    listFilterValues(mart = ensembl, filter = "phenotype_source")
    
    ## search the 'phenotype_description' filter for the term 'crohn'
    searchFilterValues(mart = ensembl, 
                       filter = "phenotype_description", 
                       pattern = "crohn")
}