computeScoreT1: Compute the score of a model/data set using a bitString to...

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

Compute the score of a model/data set using a bitString to cut the model.

Description

The bitString made of 0 and 1 allows to select a submodel from the model provided. Then, the simulator function are called to compute the objective function. The sizeFac and NAFac are penalties added to the final score as described in gaBinaryT1. The indexList and simList arguments can be provided to speed up the code otherwise, they are recomputed from the CNOlist and model.

Usage

computeScoreT1(CNOlist, model, bString, simList=NULL, indexList=NULL,
    sizeFac=0.0001, NAFac=1, timeIndex=2)

Arguments

CNOlist	a CNOlist structure, as created by makeCNOlist.
model	a model structure, as created by codereadSIF, normally pre-processed but that is not a requirement of this function.
bString	a bitstring of the same size as the number of reactions in the model above
simList	If provided, simList should be created by prep4sim, that has also already been cut to contain only the reactions to be evaluated.
indexList	If provided, indexList should contain a list of indexes of the species stimulated/inhibited/measured in the model, as created by indexFinder.
sizeFac	the scaling factor for the size term in the objective function, default to 0.0001
NAFac	the scaling factor for the NA term in the objective function, default to 1
timeIndex	the index of the time point to optimize. Must be greater or equal to 2 (1 corresponds to time=0). Must be less than the number of time points. Default is 2.

Value

score

See gaBinaryT1 for details

Author(s)

T. Cokelaer

Examples

    data(CNOlistToy,package="CellNOptR")
    data(ToyModel,package="CellNOptR")
    model <- preprocessing(CNOlistToy,ToyModel)
    score = computeScoreT1(CNOlist(CNOlistToy), model, bString=rep(1,16))

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