writeBiopax: This function writes out a biopax model.

In rBiopaxParser: Parses BioPax files and represents them in R

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.

Author(s)

Frank Kramer

Examples

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

rBiopaxParser documentation built on Nov. 8, 2020, 8:21 p.m.