runWithMart: Run a pre-formatted query with the provided "Mart" object.

In meekrob/ParasiteXML: Functions For Converting Parasite Database XML into R Code

Run a pre-formatted query with the provided "Mart" object.

Description

Run a pre-formatted query, as returned by format_BM_from_XML() to biomaRt with a "Mart" object as returned by getParamart() or useMart().

Usage

runWithMart(cll, mart)

Arguments

cll	biomaRt call as returned by format_BM_from_XML()
mart	a "Mart" object as returned by getParamart() or useMart().

Value

The query result as a dataframe.

See Also

getBM, getParamart

Examples

query = format_BM_from_XML('<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE Query>
<Query  virtualSchemaName = "parasite_mart" formatter = "TSV" header = "0" uniqueRows = "0" count = "" datasetConfigVersion = "0.6" >
  <Dataset name = "wbps_gene" interface = "default" >
     <Filter name = "biotype" value = "lincRNA"/>
     <Filter name = "species_id_1010" value = "caelegprjna13758"/>
     <Attribute name = "wbps_gene_id" />
  </Dataset>
</Query>')

library(biomaRt)
mart = getParamart()
lincs = runWithMart(query, mart)

meekrob/ParasiteXML documentation built on March 11, 2023, 10:53 a.m.