computeScoreTN {CellNOptR} | R Documentation

## Compute the score at TN 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 `gaBinaryTN`.

### Usage

    computeScoreTN(CNOlist, model, simList=NULL, indexList=NULL, simResPrev=NULL,
        bStringPrev=NULL, bStringNext=NULL, timeIndex=NULL, sizeFac=0.0001, NAFac=1, bStrings=NULL)

### 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.
`simList` | a simList as created by `prep4sim`, that has also already been cut to contain only the reactions to be evaluated. If not provided, it is recomputed automatically.
`indexList` | a list of indexes of the species stimulated/inhibited/measured in the model, as created by `indexFinder`. If not provided ,it is recomputed automatically.
`simResPrev` | Results of Previous simulation at time TN-1 step.
`bStringPrev` | the best bitString at time TN-1
`bStringNext` | the bitString to use to compute the score at time TN
`timeIndex` | Future feature will allows timeIndex to provide the exact list of indices to cut and plot. For now, it is based on the bitStrings provided.
`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
`bStrings` | list of optimised bitstrings found at the previous time points

### Value

`score` | See `gaBinaryTN` for details

### Author(s)

T. Cokelaer, S.Schrier

### Examples

        data(CNOlistToy2,package="CellNOptR")
        data(ToyModel2,package="CellNOptR")
        model <- preprocessing(CNOlistToy2, ToyModel2)
        bStringT1 = c(0,0,1,1,1,1,1,1,0,0,1,1,1,1,1,1)
        simT1<-simulateTN(CNOlist=CNOlistToy2, model=model, bStrings=list(bStringT1))

        score1 = computeScoreTN(CNOlistToy2, model, bStrings=list(bStringT1,c(1,0,1,0)))

[Package CellNOptR version 1.36.0 Index]