prep4sim: Prepare a model for simulation

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

Prepare a model for simulation

Description

Adds to the model some fields that are used by the simulation engine

Usage

prep4sim(model)

Arguments

model

a model list, as output by readSIF, normally pre-processed but that is not a requirement of this function

Details

This adds fields that are necessary for the simulation engine in a version that is extensible for constrained Fuzzy logic extension of the methods applied here (in development).

Value

this function returns a list with fields:

finalCube	stores, for each reac(row) the location of its inputs (col)
ixNeg	stores, for each reac(row) and each input (col) whether it is a negative input
ignoreCube	logical matrix of the same size as the 2 above, that tells whether the particular cell is filled or not
maxIx	row vector that stores, for each reac, the location of its output
modelname	stores the name of the model from which these fields were derived
maxInput	stores the max number of inputs observed in the model for a single reaction

Note

For internal usage since version 1.3.28

Author(s)

C. Terfve, T. Cokelaer

See Also

simulatorT1

Examples

data(ToyModel,package="CellNOptR")
ToyFields4Sim<-prep4sim(ToyModel)

saezlab/CellNOptR documentation built on April 16, 2024, 5:21 a.m.