CellNOptR (version 1.18.0)

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:

1.10.0

Date:

2014-03-13

License:

GPLv3

LazyLoad:

yes

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)