getXML: Retrieves information from the BioMart database using an XML...

Description Usage Arguments Details Author(s) Examples

View source: R/biomaRt.R

Description

DEPRECATED! - This function is a low level query function bypassing lots of biomaRts internal controls. It allows for a direct XML query to a known BioMart webservice host.

Usage

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getXML(host="http://www.ensembl.org/biomart/martservice?", xmlquery)

Arguments

host

URL to BioMart webservice, is set to http://www.ensembl.org/biomart/martservice? by default

xmlquery

XML query that needs to be send to the webservice

Details

This function has now been deprecated. Similar functionality can be achieved using the unexported function 'biomaRt:::.submitQueryXML. If you are still using this function and this affects your work, please contact the package maintainer at https://github.com/grimbough/biomaRt/issues

Author(s)

Steffen Durinck, Mike Smith

Examples

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if(interactive()){
xmlquery="<?xml version='1.0' encoding='UTF-8'?>
            <!DOCTYPE Query>
            <Query virtualSchemaName = 'default' uniqueRows = '1' 
                   count = '0' datasetConfigVersion = '0.6'>
                <Dataset name = 'hsapiens_gene_ensembl'>
                    <Attribute name = 'ensembl_gene_id'/>
                    <Filter name = 'chromosome_name' value = 'Y' />
                </Dataset>
            </Query>"
getXML(host = "www.ensembl.org/biomart/martservice?", xmlquery = xmlquery)
}

biomaRt documentation built on Nov. 1, 2018, 3:34 a.m.