getBM {biomaRt}R Documentation

Retrieves information from the BioMart database

Description

This function retrieves information from the BioMart database

Usage

getBM(attributes, filters, values, mart, curl = NULL, output = "data.frame", list.names = NULL, na.value = NA)

Arguments

attributes Attributes you want to retrieve. A possible list of attributes can be retrieved using the function listAttributes.
filters Filters 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. list of affy IDs
mart object of class Mart, containing connections to the BioMart databases. You can creat such an object using the function useMart and update the mart object by selecting a dataset using the function useDataset.
curl An optional 'CURLHandle' object, that can be used to speed up getBM when used in a loop.
output Determines the output of getBM which can be either a data.frame (default) or a list.
list.names In case a list was selected as output the different elements in the list can be given user defined names with this argument
na.value In case a list was selected as output, the value of na.value will used when missing elements are present in the output

Author(s)

Steffen Durinck, http://www.esat.kuleuven.ac.be/~sdurinck

Examples

if(interactive()){
mart <- useMart("ensembl")
datasets <- listDatasets(mart)
mart<-useDataset("hsapiens_gene_ensembl",mart)
getBM(attributes=c("affy_hg_u95av2","hgnc_symbol","chromosome_name","band"),filters="affy_hg_u95av2",values=c("1939_at","1503_at","1454_at"), mart=mart)

}

[Package biomaRt version 1.8.2 Index]