simulatorDT: Discrete time simulation of a boolean model

In saezlab/CNORdt: Add-on to CellNOptR: Discretized time treatments

Description

Simulates multiple time points within C (for speed).

Usage

simulatorDT(CNOlist, model, simList, indices, boolUpdates,
prevSim=NULL)

Arguments

CNOlist	A CNOlist.
model	A model that only contains the reactions to be evaluated.
simList	A simList as created by prep4sim, that has also already been cut to contain only the reactions to be evaluated.
indices	An indexList as created by indexFinder.
boolUpdates	The number of update rounds the simulator should run for.
prevSim	The results from simulatorT0 can be used here as initial conditions.

Value

A 3-dimensional array that gives the value of all species under each condition at each update (conditions, species, update).

Author(s)

A. MacNamara

See Also

gaBinaryDT, getFitDT

Examples

# this computes the output of the full model, 
# which is normally not done on a stand alone basis,
# but if you have a model and would like to visualise 
# its output compared to your data, then this is what you should do.

library(CellNOptR)
library(CNORdt)
data(CNOlistPB, package="CNORdt")
data(modelPB, package="CNORdt")

indexOrig <- indexFinder(CNOlistPB, modelPB, verbose=TRUE)
fields4Sim <- prep4sim(modelPB)
boolUpdates=10

simResults <- simulatorDT(
  CNOlist=CNOlistPB,
  model=modelPB,
  simList=fields4Sim,
  indices=indexOrig,
  boolUpdates=boolUpdates
)
simResults = convert2array(simResults, dim(CNOlistPB$valueSignals[[1]])[1],
length(modelPB$namesSpecies), boolUpdates)

saezlab/CNORdt documentation built on May 17, 2019, 1:59 p.m.