CellNOptR: CellNOptR-package – R documentation

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CellNOptR-package

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

# 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)

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