CellNOptR: findNONC – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

findNONC

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

Examples

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

CellNOptR

Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

v1.36.0

GPL-3

Authors

T.Cokelaer, F.Eduati, A.MacNamara, S.Schrier, C.Terfve, E.Gjerga, A.Gabor

Initial release

2018-11-08