CNORdt (version 1.14.0)

computeScoreDT: Compute the score of a model/data (time-course) set using a bitString to cut the model.

Description

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

Usage

computeScoreDT(CNOlist, model, bString, simList=NULL, indexList=NULL,
sizeFac=0.0001, NAFac=1, boolUpdates, lowerB=lowerB, upperB=upperB)

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 bit string of the same size as the number of reactions in the model above.

simList

If provided, simList should be created by prep4sim, and 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.

boolUpdates

The number of synchronous updates performed by the boolean simulator.

lowerB

The lower bound for the optimized value of the scaling factor.

upperB

The upper bound for the optimized value of the scaling factor.

Value

score

See gaBinaryT1 for details.

Examples

library(CellNOptR)
library(CNORdt)
data(CNOlistPB, package="CNORdt")
data(modelPB, package="CNORdt")

# pre-process model
model = preprocessing(CNOlistPB, modelPB)

# compute score
score = computeScoreDT(CNOlistPB, model, bString=rep(1,16),
boolUpdates=10, lowerB=0.8, upperB=10)