computeScoreTN: Compute the score at TN of a model/data set using a bitString...

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

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)))

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