getBM: 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, checkFilters = TRUE, verbose = FALSE, uniqueRows = TRUE, bmHeader = FALSE)

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.

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.

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.

bmHeader

Boolean to indicate if the result retrieved from the BioMart server should include the data headers or not, defaults to FALSE. This should only be switched on if the default behavior results in errors, setting to on might still be able to retrieve your data in that case

Value

data.frame. There is no implicit mapping between its rows and the function arguments (e.g. filters, values), therefore make sure to have the relevant identifier(s) returned by specifying them in attributes. See Examples.

Examples

Run this code

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)
# rows are sorted by `affy_hg_u95av2`, and in different order than the `values` argument
}

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