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


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Documentation for package ‘CellNOptR’ version 1.22.0

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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.
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.
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 --

ToyModel Toy model
ToyModel2 Toy model

-- W --

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.