This function reads in a Biopax .owl file

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

1
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

1
2
 ## Not run: biopax = readBiopax(file="biopaxmodel.owl")
 ## Not run: biopax 

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