listFilters {biomaRt} | R Documentation |
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.
listFilters(mart, what = c("name", "description")) searchFilters(mart, pattern)
mart |
object of class |
what |
character vector indicating what information to display about the
available filters. Valid values are
|
pattern |
Character vector defining the regular expression ( |
Steffen Durinck, Mike Smith
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') }