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

## Documentation for package ‘CellNOptR’ version 1.4.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

CellNOptR-package | R version of CellNOptR, boolean features
CellNOptR | R version of CellNOptR, boolean features
checkSignals | Check the CNOlist and model matching
CNOlist | Class '"CNOlist"'
CNOlist,ANY | Class '"CNOlist"'
CNOlist-class | Class '"CNOlist"'
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
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.
cSimulator | C-implementation of simulatorT1.
cutAndPlot | Interface to cutAndPlotResults functions.
cutAndPlotResultsT1 | Plot the results of an optimisation at t1
cutAndPlotResultsT2 | Plot the results of an optimisation at t2 (deprecated since v1.3.28; use cutAndPlotResultsTN instead)
cutAndPlotResultsTN | Plot the results of an optimisation at tN
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
defaultParameters | Create a list of default parameters
DreamModel | Model used for the DREAM3 challenge
expandGates | Expand the gates of a model
findNONC | Find the indexes of the non-observable and non controllable species
gaBinaryT1 | Genetic algorithm used to optimise a model
gaBinaryT2 | Genetic algorithm for time point 2
gaBinaryTN | Genetic algorithm for time point N
getFit | Compute the score of a model
graph2sif | Convert graph to SIF
indexFinder | Finds the indices, in the model fields, of the species that are measured/inhibited/stimulated
makeCNOlist | Make a CNOlist structure
mapBack | Map an optimised model back onto the PKN model.
model2sif | Convert a model object in sif format
normaliseCNOlist | Normalisation for boolean modelling.
plot-method | plot a '"CNOlist"' object - methods
plot.CNOlist | plot a '"CNOlist"' object - methods
plotCNOlist | Plot the data in a CNOlist
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
readMIDAS | Reads in a CSV MIDAS file
readMidas | Reads in a CSV MIDAS file
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
show-method | Class '"CNOlist"'
sif2graph | Convert sif to graph
simulateT1 | deprecated since version 1.3.28. Cut and simulation of a boolean model at t1
simulateTN | Cut and simulation of a boolean model at t1
simulatorT0 | Simulation of a boolean model
simulatorT1 | Simulation of a boolean model
simulatorT2 | Deprecated since 1.3.28. Use simulateTN function instead. Simulation of a boolean model for time 2
simulatorTN | Simulation of a boolean model at any time points dependent on a previous one.
ToyModel | Toy model
ToyModel2 | Toy model
writeDot | Write a model, and attached features, to a dot file
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
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.