simulateT1: deprecated since version 1.3.28. Cut and simulation of a...

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

deprecated since version 1.3.28. Cut and simulation of a boolean model at t1. Use simulateTN instead.

Description

This function cuts a model according to a bitstring optimised at T1, and simulates the model accordingly.

Usage

simulateT1(CNOlist, model, bStringT1, simList, indexList)

Arguments

CNOlist	a CNOlist object
model	a full model
bStringT1	a bitstring to cut the model, as output by gaBinaryT1 (i.e. a vector of 1s and 0s, of length equal to the number of reactions in the model)
simList	a list of additional fields for simulation as created by prep4sim, corresponding to the full model
indexList	a list of indexes as created by indexFinder

Details

This function is a wrapper for simulatorT1, that cuts the model before simulating it

Value

a matrix of simulated values, including all species in the model, i.e. to be used as input of gaBinaryTN (not implemented here) but not to be used directly in plotOptimResults.

Author(s)

C.Terfve

See Also

cutAndPlotOptimResultsT1, simulatorT1

Examples

# This will compute the output of a random model obtained by randomly selecting
# which gates of the initial models are included.

data(CNOlistToy,package="CellNOptR")
data(ToyModel,package="CellNOptR")

indicesToy<-indexFinder(CNOlistToy,ToyModel,verbose=FALSE)
ToyFields4Sim<-prep4sim(ToyModel)

simRes<-simulateT1(
	CNOlist=CNOlistToy, 
	model=ToyModel, 
	bStringT1=round(runif(length(ToyModel$reacID))), 
	simList=ToyFields4Sim, 
	indexList=indicesToy)

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