preprocessing: Performs the pre-processing steps

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

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).

Details

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

Value

the new model

Author(s)

T. Cokelaer

See Also

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

Examples

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

cokelaer/CellNOptR documentation built on May 27, 2019, 8:44 a.m.