readBiopax: This function reads in a Biopax .owl file

In rBiopaxParser: Parses BioPax files and represents them in R

Description

This function reads in a Biopax .owl file and generates the internal data.frame format used in this package. This function can take a while with really big Biopax files like NCIs Pathway Interaction Database or Reactome. In almost every case this is your starting point. Returns a biopax model, which is a list with named elements:

df

The data.frame representing the biopax in R

ns_rdf

RDF Namespace

ns_owl

OWL Namespace

ns_bp

Biopax Namespace

file

File name

Usage

readBiopax(file, verbose = TRUE)

Arguments

file	string. File name
verbose	logical. Output messages about how parsing is going and so on.

Value

A biopax model

Author(s)

Frank Kramer

Examples

## Not run: biopax = readBiopax(file="biopaxmodel.owl")
## Not run: biopax 
#'  # load data and retrieve wnt pathway
data(biopaxexample)

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