computeScoreT1 {CellNOptR} | R Documentation

## 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))

[Package CellNOptR version 1.38.0 Index]