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


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Documentation for package ‘CellNOptR’ version 1.26.0

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

CellNOptR-package R version of CellNOptR, boolean features

-- 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.
crossInhibitedData If an inhibitor is also a measured species, replace the data with NA (when inhibited)
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 --

indexFinder Finds the indices, in the model fields, of the species that are measured/inhibited/stimulated
internals List of CellNOptR internal functions.

-- 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.
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"'
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.