rBiopaxParser (version 2.10.0)

writeBiopax: This function writes out a biopax model.

Description

This function writes out a biopax model, as generated by readBiopax, to either a file or returns the xmlTree if file is omitted.

Usage

writeBiopax(biopax, file = "", verbose = TRUE, overwrite = FALSE, namespaces = list(rdf = "http://www.w3.org/1999/02/22-rdf-syntax-ns#", bp = "http://www.biopax.org/release/biopax-level2.owl#", rdfs = "http://www.w3.org/2000/01/rdf-schema#", owl = "http://www.w3.org/2002/07/owl#", xsd = "http://www.w3.org/2001/XMLSchema#"))

Arguments

biopax

A biopax model as generated by readBiopax

file

A string giving a file name.

verbose

logical

overwrite

logical, if TRUE an already existing file will be overwritten, otherwise an error is thrown

namespaces

A list of namespaces to use for the generated XML/RDF file

Value

Returns the xmlTree object generated from the biopax model. If a filename is supplied the XML is written to this file.

Examples

# load data
 data(biopax2example)
 ## Not run: writeBiopax(biopax, file="mybiopax.owl")