writeBiopax: This function writes out a biopax model.

Description Usage Arguments Value Author(s) Examples

View source: R/writeBiopax.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

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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

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

frankkramer-lab/rBiopaxParser documentation built on July 19, 2020, 9:49 a.m.