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CellNOptR (version 1.18.0)

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

Description

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

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Version

Version

1.18.0

License

GPL-3

Maintainer

T Cokelaer

Last Published

February 15th, 2017

Functions in CellNOptR (1.18.0)

CNOlistToy

Toy data
preprocessing

Performs the pre-processing steps
randomizeCNOlist

add noise to the data contained in a CNOlist.
simulatorTN

Simulation of a boolean model at any time points dependent on a previous one.
cSimulator

C-implementation of simulatorT1.
plotCNOlistPDF

Plots a CNOlist into a pdf file.
LiverDREAM

Model used for the DREAM3 challenge
CNOlist-class

Class "CNOlist"
defaultParameters

Create a list of default parameters
CNOlist-methods

List of CNOlist-class methods
compressModel

Compress a model
CNOlistToy2

Toy data with 2 time points
buildBitString

Build the final bit string vector and times vector based on a list of optimised bit strings at different time points.
plotOptimResults

Plot the data and simulated values
simulateTN

Cut and simulation of a boolean model at t1
sif2graph

Convert sif to graph
CNORbool

Simple Boolean analysis standalone
findNONC

Find the indexes of the non-observable and non controllable species
graph2sif

Convert graph to SIF
computeScoreTN

Compute the score at TN of a model/data set using a bitString to cut the model.
writeMIDAS

Write a CNOlist structure into a MIDAS file
exhaustive

Exhaustive search over the optimisation of a PKN model on MIDAS data.
computeScoreT1

Compute the score of a model/data set using a bitString to cut the model.
residualError

Compute the residual error for a dataset
makeCNOlist

Make a CNOlist structure
CNOdata

Get data from a CellNOpt data repository
checkSignals

Check the CNOlist and model matching
cutAndPlot

Interface to cutAndPlotResults functions.
CNORwrap

CNOR analysis wrapper
gaBinaryT2

Genetic algorithm for time point 2
cutSimList

Cut a simList structure according to a bitstring
mapBack

Map an optimised model back onto the PKN model.
writeDot

Write a model, and attached features, to a dot file
cutModel

Cut a model structure according to a bitstring
gaBinaryTN

Genetic algorithm for time point N
gaBinaryT1

Genetic algorithm used to optimise a model
model2sif

Convert a model object in sif format
plotCNOlistLargePDF

Plots a CNOlist into a pdf file, for lists with many conditions.
model2igraph

Convert a model object to a igraph object
expandGates

Expand the gates of a model
simulatorT0

Simulation of a boolean model
writeReport

Write a report of a CellNOptR analysis
writeNetwork

Write a previous knowledge network model to a sif file (with attribute files), as well as a dot file
simulatorT1

Simulation of a boolean model
CNOlistToyMMB

Toy data
CNOlistDREAM

Data used for the DREAM3 challenge
prep4sim

Prepare a model for simulation
ToyModel

Toy model
plotOptimResultsPDF

Plot the data and simulated values in a pdf file
CellNOptR-package

R version of CellNOptR, boolean features
readSBMLQual

Read a SBMLQual document and returns a SIF object (as returned by readSIG
ToyModel2

Toy model
cutAndPlotResultsT1

Plot the results of an optimisation at t1
readMIDAS

Reads in a CSV MIDAS file
plotCNOlistLarge

Plot the data in a CNOlist, for lists with many conditions.
plotOptimResultsPan

Plots the data and simulated values from any CellNOptR formalism
plotModel

Plot a model
plotCNOlist2

Another version of plotCNOlist that allows to plot 2 cnolist in the same layout to compare them. This function uses ggplot2 library. It is recommended for small data sets (about 15 species).
cutAndPlotResultsTN

Plot the results of an optimisation at tN
simulateT1

deprecated since version 1.3.28. Cut and simulation of a boolean model at t1. Use simulateTN instead.
readSIF

Read a SIF file and create a model object
cutCNOlist

Cut a CNOlist structure according to a model
plotFit

Plot the evolution of an optimisation
normaliseCNOlist

Normalisation for boolean modelling.
getFit

Compute the score of a model
cutNONC

Cuts the non-observable/non-controllable species from the model
simulatorT2

Deprecated since 1.3.28. Use simulateTN function instead. Simulation of a boolean model for time 2
writeSIF

Convert a model into a SIF format and save the result in a file.
writeScaffold

Writes the scaffold network to a sif file (with attributes) and to a dot file
plotCNOlist

Plot the data in a CNOlist
internals

List of CellNOptR internal functions.
indexFinder

Finds the indices, in the model fields, of the species that are measured/inhibited/stimulated
plot-method

plot a "CNOlist" object - methods