CellNOptR-package {CellNOptR} | R Documentation

## R version of CellNOptR, boolean features

### Description

This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data collected upon perturbation of some of the nodes in the network.

### Details

Package: | CellNOptR
Type: | Package
Version: | 1.25.1
Date: | 2018-01-10
License: | GPLv3
LazyLoad: | yes

### Author(s)

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

Maintainer: A. Gabor<gabor.attila87@gmail.com>, until 2018-01-18: T. Cokelaer <cokelaer@ebi.ac.uk>

### References

J. Saez-Rodriguez, L. G. Alexopoulos, J. Epperlein, R. Samaga, D. A. Lauffenburger, S. Klamt and P. K. Sorger. Discrete logic modeling as a means to link protein signaling networks with functional analysis of mammalian signal transduction, Molecular Systems Biology, 5:331, 2009.

### Examples

    library(CellNOptR)

    # quick 1 time point optimisation of a Prior Knowledge Network to MIDAS data.
    data(CNOlistToy,package="CellNOptR")
    data(ToyModel,package="CellNOptR")

    pknmodel = ToyModel
    cnolist = CNOlist(CNOlistToy)
    model = preprocessing(cnolist, pknmodel)
    results = gaBinaryT1(cnolist, model, verbose=FALSE)
    plotFit(results)
    cutAndPlot(cnolist, model, list(results$bString))

    # Same as above and HTML report
    CNORwrap(name="Toy",
        namesData=list(CNOlist="ToyData",model="ToyModel"),
        data=CNOlistToy, model=pknmodel)

[Package CellNOptR version 1.26.0 Index]