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

## Documentation for package ‘CellNOptR’ version 1.36.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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
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 --

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.