pathway2RegulatoryGraph: This function generates the regulatory graph from the...
In frankkramer-lab/rBiopaxParser: Parses BioPax files and represents them in R

Description Usage Arguments Value Author(s) Examples

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

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.

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

`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

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

Frank Kramer

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