findNONC: Find the indexes of the non-observable and non controllable...

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

Find the indexes of the non-observable and non controllable species

Description

This function finds the indexes of the non-observable and non controllable species and returns the indices, in the model, of the species to remove

Usage

findNONC(model, indexes, verbose=FALSE)

Arguments

model	a model structure, as created by readSIF
indexes	a list of indexes of the species stimulated/inhibited/measured, as created by indexFinder from a model.
verbose	verbose option (default to FALSE)

Details

This function uses the function floyd.warshall.all.pairs.sp from the package RBGL. Non observable nodes are those that do not have a path to any measured species in the model, whereas non controllable nodes are those that do not receive any information from a species that is perturbed in the data.

Value

a vector of indices of species to remove

Note

No need to call this function directly since version 0.99.24. Use preprocessing instead.

Author(s)

C. Terfve

See Also

cutNONC, indexFinder, readSIF

Examples

    data(CNOlistToy, package="CellNOptR")
    data(ToyModel, package="CellNOptR")
    checkSignals(CNOlistToy, ToyModel)
    indicesToy <- indexFinder(CNOlistToy, ToyModel)
    ToyNCNOindices <- findNONC(ToyModel, indicesToy)

saezlab/CellNOptR documentation built on April 16, 2024, 5:21 a.m.