getBM {biomaRt}R Documentation

Retrieves information from the BioMart database

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

getBM(attributes, filters = "", values = "", mart, curl = NULL, output = "data.frame", list.names = NULL, na.value = NA, checkFilters = TRUE, verbose = FALSE, uniqueRows = 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.
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
checkFilters Sometimes attributes where a value needs to be specified, for example upstream_flank with value 20 for obtaining upstream sequence flank regions of length 20bp, are treated as filters in BioMarts. To enable such a query to work, one must specify the attribute as a filter and set checkFilters = FALSE for the query to work.
verbose When using biomaRt in webservice mode and setting verbose to TRUE, the XML query to the webservice will be printed. Alternatively in MySQL mode the MySQL query will be printed.
uniqueRows If the result of a query contains multiple identical rows, setting this argument to TRUE (default) will result in deleting the duplicated rows in the query result at the server side.

Author(s)

Steffen Durinck, http://www.stat.berkeley.edu/~steffen

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 1.16.0 Index]