CellNOptR-package: R version of CellNOptR, boolean features

Description Details Author(s) References Examples

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<[email protected]>, until 2018-01-18: T. Cokelaer <[email protected]>

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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
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)

CellNOptR documentation built on May 2, 2018, 4:23 a.m.