CellNOptR (version 1.18.0)

preprocessing: Performs the pre-processing steps

Description

This function performs any of the following preprocessing steps:

1. removes Non-Controllable and Non-Observables nodes
2. compress the model
3. and-gates expansion

Usage

preprocessing(data, model, cutNONC=TRUE, compression=TRUE, expansion=TRUE, ignoreList=NA, maxInputsPerGate=2, verbose=TRUE)

Arguments

data

the CNOlist that contains the data that you will use

model

the model object as returned by readSIF

cutNONC

Removes the NONC nodes using cutNONC and findNONC (Default is TRUE).

compression

Compress the model using compressModel (Default is TRUE).

expansion

Add and gates using expandGates (Default is TRUE).

ignoreList

list of reactions indices to ignore in the expansion step.

maxInputsPerGate

used by the expandGates function to set maximum inputs per and gates.

verbose

verbose option (Default is TRUE).

Value

the new model

Details

The function can apply any or none of the pre-processing steps. It returns the new model and the indices returned by indexFinder.

See Also

readSIF, readMIDAS, cutNONC, findNONC, compressModel, expandGates.

Examples

data(ToyModel,package="CellNOptR")
data(CNOlistToy,package="CellNOptR")
model = preprocessing(CNOlistToy, ToyModel, cutNONC=FALSE)