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

Documentation for package ‘CellNOptR’ version 1.53.2

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B C D E F G I L M N P R S T W

CellNOptR-package

R version of CellNOptR, boolean features

-- B --

build_sif_table_from_rule

Build a SIF table from a logic rule written in a string

-- C --

CellNOptR	R version of CellNOptR, boolean features
checkSignals	Check the CNOlist and model matching
CNOdata	Get data from a CellNOpt data repository
cnodata	Get data from a CellNOpt data repository
CNOlist	Class '"CNOlist"'
CNOlist-class	Class '"CNOlist"'
CNOlist-methods	List of CNOlist-class methods
CNOlistDREAM	Data used for the DREAM3 challenge
CNOlistToy	Toy data
CNOlistToy2	Toy data with 2 time points
CNORbool	Simple Boolean analysis standalone
CNORwrap	CNOR analysis wrapper
compatCNOlist	List of CNOlist-class methods
compatCNOlist,CNOlist	List of CNOlist-class methods
compatCNOlist-method	Class '"CNOlist"'
compressModel	Compress a model
computeScoreT1	Compute the score of a model/data set using a bitString to cut the model.
computeScoreTN	Compute the score at TN of a model/data set using a bitString to cut the model.
createAndRunILP	Creating and running the ILP problem.
createILPBitstringAll	Reading the optimal solutions as bitstrings.
create_binaries	Defining the set of binary variables for the ILP implementation of CellNOptR.
crossInhibitedData	If an inhibitor is also a measured species, replace the data with NA (when inhibited)
crossvalidateBoolean	k-fold crossvalidation for Boolean model.
cutAndPlot	Interface to cutAndPlotResults functions.
cutAndPlotResultsT1	Plot the results of an optimisation at t1
cutAndPlotResultsTN	Plot the results of an optimisation at tN
cutCNOlist	Cut a CNOlist structure according to a model
cutModel	Cut a model structure according to a bitstring
cutNONC	Cuts the non-observable/non-controllable species from the model
cutSimList	Cut a simList structure according to a bitstring

-- D --

defaultParameters	Create a list of default parameters
DreamModel	Model used for the DREAM3 challenge

-- E --

exhaustive	Exhaustive search over the optimisation of a PKN model on MIDAS data.
expandGates	Expand the gates of a model

-- F --

findNONC

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

-- G --

gaBinaryT1	Genetic algorithm used to optimise a model
gaBinaryTN	Genetic algorithm for time point N
getCues	List of CNOlist-class methods
getCues,CNOlist	List of CNOlist-class methods
getCues-method	Class '"CNOlist"'
getFit	Compute the score of a model
getInhibitors	List of CNOlist-class methods
getInhibitors,CNOlist	List of CNOlist-class methods
getInhibitors-method	Class '"CNOlist"'
getSignals	List of CNOlist-class methods
getSignals,CNOlist	List of CNOlist-class methods
getSignals-method	Class '"CNOlist"'
getStimuli	List of CNOlist-class methods
getStimuli,CNOlist	List of CNOlist-class methods
getStimuli-method	Class '"CNOlist"'
getTimepoints	List of CNOlist-class methods
getTimepoints,CNOlist	List of CNOlist-class methods
getTimepoints-method	Class '"CNOlist"'
getVariances	List of CNOlist-class methods
getVariances,CNOlist	List of CNOlist-class methods
getVariances-method	Class '"CNOlist"'
getVariances-method	List of CNOlist-class methods
graph2sif	Convert graph to SIF

-- I --

ilpBinaryT1	ILP method used to optimise a model
ilpBinaryT2	ILP method used to optimise a model
ilpBinaryTN	ILP method used to optimise a model
indexFinder	Finds the indices, in the model fields, of the species that are measured/inhibited/stimulated
internals	List of CellNOptR internal functions.
invokeCPLEX	Solving the ILP problem with CPLEX.

-- L --

length	List of CNOlist-class methods
length,CNOlist	List of CNOlist-class methods
length-method	Class '"CNOlist"'
length-method	List of CNOlist-class methods

-- M --

makeCNOlist	Make a CNOlist structure
mapBack	Map an optimised model back onto the PKN model.
model2igraph	Convert a model object to a igraph object
model2sif	Convert a model object in sif format

-- N --

normaliseCNOlist

Normalisation for boolean modelling.

-- P --

pknmodel	pknmodel
plot-method	Class '"CNOlist"'
plot-method	List of CNOlist-class methods
plot-method	plot a '"CNOlist"' object - methods
plot.CNOlist	plot a '"CNOlist"' object - methods
plotCNOlist	Plot the data in a CNOlist
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).
plotCNOlistLarge	Plot the data in a CNOlist, for lists with many conditions.
plotCNOlistLargePDF	Plots a CNOlist into a pdf file, for lists with many conditions.
plotCNOlistPDF	Plots a CNOlist into a pdf file.
plotFit	Plot the evolution of an optimisation
plotModel	Plot a model
plotOptimResults	Plot the data and simulated values
plotOptimResultsPan	Plots the data and simulated values from any CellNOptR formalism
plotOptimResultsPDF	Plot the data and simulated values in a pdf file
prep4Sim	Prepare a model for simulation
prep4sim	Prepare a model for simulation
preprocessing	Performs the pre-processing steps

-- R --

randomize	List of CNOlist-class methods
randomize,CNOlist	List of CNOlist-class methods
randomize-method	Class '"CNOlist"'
randomize-method	List of CNOlist-class methods
randomizeCNOlist	add noise to the data contained in a CNOlist.
readBND	Read network from BND file
readBNET	Read network from BNET file
readErrors	List of CNOlist-class methods
readErrors,CNOlist	List of CNOlist-class methods
readErrors-method	Class '"CNOlist"'
readMIDAS	Reads in a CSV MIDAS file
readMidas	Reads in a CSV MIDAS file
readSBMLQual	Read a SBMLQual document and returns a SIF object (as returned by readSIG
readSIF	Read a SIF file and create a model object
readSif	Read a SIF file and create a model object
residualError	Compute the residual error for a dataset

-- S --

setSignals<-	List of CNOlist-class methods
setSignals<-,CNOlist	List of CNOlist-class methods
setSignals<--method	Class '"CNOlist"'
setSignals<--method	List of CNOlist-class methods
sif2graph	Convert sif to graph
simulateTN	Cut and simulation of a boolean model at t1
simulatorT0	Simulation of a boolean model
simulatorT1	Simulation of a boolean model
simulatorTN	Simulation of a boolean model at any time points dependent on a previous one.

-- T --

toSBML	Export the network to SBML-qual format
ToyModel	Toy model
ToyModel2	Toy model

-- W --

writeDot	Write a model, and attached features, to a dot file
writeErrors	List of CNOlist-class methods
writeErrors,CNOlist	List of CNOlist-class methods
writeErrors-method	Class '"CNOlist"'
writeFile	Writing the ILP problem.
writeMIDAS	Write a CNOlist structure into a MIDAS file
writeNetwork	Write a previous knowledge network model to a sif file (with attribute files), as well as a dot file
writeObjectiveFunction	Writing the objective function for the ILP implementation of CellNOptR.
writeReport	Write a report of a CellNOptR analysis
writeScaffold	Writes the scaffold network to a sif file (with attributes) and to a dot file
writeSIF	Convert a model into a SIF format and save the result in a file.
writeSif	Convert a model into a SIF format and save the result in a file.
write_bounds	Writing the set of boundaries for each integer variable for the ILP implementation of CellNOptR.
write_constraints	Writing the set of constraints for the ILP implementation of CellNOptR.