model2sif: Convert a model object in sif format

In CellNOptR: Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Description

This function receives as input a model object and converts it to the cytoscape sif format. It can be used to convert either the whole model (before or after pre-processing) or the optimized one (if the corresponding bitString in provided). The resulting table can also be saved in a sif file.

Usage

model2sif(model,optimRes=NA,writeSif=FALSE, filename="Model")

Arguments

model	the model as generated using readSIF
optimRes	the output of the optimisation (as obtained using gaBinaryT1), default set to NA the whole model in converted
writeSif	it writeSif=FALSE (default) the sif file is not saved. If writeSif=TRUE it is saved.
filename	the name of the sif file saved if writeSif=TRUE. Default is Model.sif.

Details

All links in the model are converted in sif format that is sourceNode-tab-sign-tab-targetNode. If there are ANDs, they are converted using dummy nodes called and# (e.g. A+B=C will be A-tab-1-tab-and1; B-tab-1-tab-and1; and1-tab-1-tab-C).

Value

sifFile

a table with all the links in the model in the format sourceNode-tab-sign-tab-targetNode

Author(s)

F.Eduati

See Also

graph2sif, sif2graph, readSIF,

CellNOptR documentation built on Nov. 8, 2020, 6:58 p.m.