CellNOptR (version 1.18.0)

computeScoreT1: 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

Examples

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