Description Usage Arguments Value Author(s) Examples

View source: R/computeScoreDT.R

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.

1 2 | ```
computeScoreDT(CNOlist, model, bString, simList=NULL, indexList=NULL,
sizeFac=0.0001, NAFac=1, boolUpdates, lowerB=lowerB, upperB=upperB)
``` |

`CNOlist` |
A CNOlist structure, as created by |

`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 |

`indexList` |
If provided, indexList should contain a list of indexes of the species stimulated/inhibited/measured in the
model, as created by |

`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. |

`score` |
See |

A. MacNamara

1 2 3 4 5 6 7 8 9 10 11 |

saezlab/CNORdt documentation built on Jan. 10, 2018, 12:57 a.m.

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