rBiopaxParser (version 2.10.0)

pathway2RegulatoryGraph: This function generates the regulatory graph from the activations/inhibitions of a pathway in a biopax model.

Description

This functions builds a graph from the pathway components of the supplied pathway. Only instances of class 'control' are considered, this leads a functinal graph with all edges either representing activations or inhibitions. No transports, no translocation, etc. If desired complexes can be split up into several nodes, this can sometimes lead to a more complex and cluttered graph. There can not be multiple edges between 2 nodes. Whenever duplicated edges are generated (especially by splitting up complexes) a warning is thrown.

Usage

pathway2RegulatoryGraph(biopax, pwid, expandSubpathways = TRUE, splitComplexMolecules = TRUE, useIDasNodenames = FALSE, verbose = TRUE)

Arguments

biopax

A biopax model

pwid

string

expandSubpathways

logical. If TRUE subpathways are expanded into this graph, otherwise only this very pathway is used.

splitComplexMolecules

logical. If TRUE every complex is split up into its components. This leads to splitting a single node with name of the complex into several nodes with names of the components, these components all have identical edges.

useIDasNodenames

logical. If TRUE nodes of the graph are named by their molecule IDs instead of using the NAME property. This can help with badly annotated/formatted databases.

verbose

logical

Value

Returns the representing the regulatory graph of the supplied pathway in a node-edge-list graph.

Examples

# load data
 data(biopaxexample)
 pwid1 = "pid_p_100002_wntpathway"
 pwid2 = "pid_p_100146_hespathway"
 mygraph = pathway2RegulatoryGraph(biopax, pwid1)
 plotRegulatoryGraph(mygraph)