getBMlist: Retrieves information from the BioMart database

In biomaRt: Interface to BioMart databases (i.e. Ensembl)

Description

This function is the main biomaRt query function. Given a set of filters and corresponding values, it retrieves the user specified attributes from the BioMart database one is connected to

Usage

getBMlist(attributes, filters = "", values = "", mart, 
list.names = NULL, na.value = NA, verbose = FALSE, giveWarning = TRUE)

Arguments

attributes	Attributes you want to retrieve. A possible list of attributes can be retrieved using the function listAttributes.
filters	Filters (one or more) that should be used in the query. A possible list of filters can be retrieved using the function listFilters.
values	Values of the filter, e.g. vector of affy IDs. If multiple filters are specified then the argument should be a list of vectors of which the position of each vector corresponds to the position of the filters in the filters argument.
mart	object of class Mart, created with the useMart function.
list.names	names for objects in list
na.value	value to give when result is empty
verbose	When using biomaRt in webservice mode and setting verbose to TRUE, the XML query to the webservice will be printed.
giveWarning	Gives a warning about best practices of biomaRt and recommends using getBM instead of getBMlist

Author(s)

Steffen Durinck

Examples

if(interactive()){
mart <- useMart("ensembl")
datasets <- listDatasets(mart)

}

Example output

biomaRt documentation built on Feb. 11, 2021, 2:01 a.m.