searchFilterValues {biomaRt} | R Documentation |
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.
listFilterValues(mart, filter) searchFilterValues(mart, filter, pattern)
mart |
object of class |
filter |
The name of the filter whose options should be listed or searched. You
can list available filters via |
pattern |
Character vector defining the regular expression ( |
Mike Smith
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") }