pathway2RegulatoryGraph {rBiopaxParser} | R Documentation |
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)