Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/preprocessing.R

This function performs any of the following preprocessing steps:

removes Non-Controllable and Non-Observables nodes

compress the model

and-gates expansion

1 2 |

`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). |

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

the new model

T. Cokelaer

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

1 2 3 | ```
data(ToyModel,package="CellNOptR")
data(CNOlistToy,package="CellNOptR")
model = preprocessing(CNOlistToy, ToyModel, cutNONC=FALSE)
``` |

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