getBMlist: Retrieves information from the BioMart database

Description Usage Arguments Author(s) Examples

View source: R/biomaRt.R

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

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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

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

}

Example output



biomaRt documentation built on Nov. 8, 2020, 5:07 p.m.