pathway2AdjacancyMatrix: This function generates an adjacency matrix from the...

In rBiopaxParser: Parses BioPax files and represents them in R

Description

This function generates an adjacency matrix from the activations/inhibitions of a pathway in a biopax model.

This function internally first calls pathway2RegulatoryGraph, then converts the regulatory graph to an adjacency matrix. See pathway2RegulatoryGraph for more details.

Usage

pathway2AdjacancyMatrix(
  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 adjacency matrix representing the regulatory graph of the supplied pathway.

Author(s)

Frank Kramer

Examples

 # load data
 data(biopaxexample)
 pwid1 = "pid_p_100002_wntpathway"
 pwid2 = "pid_p_100146_hespathway"
 pathway2AdjacancyMatrix(biopax, pwid1)

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