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This function performs the optimisation of a PKN model to a CNOlist data set. It optimises each time point found in the data and returns the processed model as well as a list of optimised bitstring corresponding to each time points that has been optimised.
● Data Source:
BioConductor
● Keywords:
● Alias: CNORbool
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This function is a wrapper around the whole CNOR analysis, it performs the following steps:
● Data Source:
BioConductor
● Keywords:
● Alias: CNORwrap
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This function fetch a file from the URL provided (default is http://www.ebi.ac.uk~/cokelaer/cellnopt/data/_downloads) and save it into a temporary file.
● Data Source:
BioConductor
● Keywords:
● Alias: CNOdata
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This function takes as input the filename of a MIDAS file (or the list returned by makeCNOlist) and returns an instance of CNOlist class. It provides an object oriented approach to manipulate CNOlist. This function calls readMIDAS and makeCNOlist.
● Data Source:
BioConductor
● Keywords: classes
● Alias: CNOlist-class
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CNOlist is a class with a set of methods described here below.
● Data Source:
BioConductor
● Keywords: CNOlist, methods
● Alias: CNOlist-methods
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This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data collected upon perturbation of some of the nodes in the network.
● Data Source:
BioConductor
● Keywords: package
● Alias: CellNOptR, CellNOptR-package
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This function takes as input a list of vectors (can be only one). Each vector represents an optimised bit string at a different time point (as returned by the gaBinary functions). The first optimised bit string have the same length as the model to be optimised. The length of the following vectors corresponds to the number of zeros found in the previous bitstring. For instance, the following list of bit strings bStrings = list(c(1,1,1,0,0,0), c(1,0,0)) is correct whereas bStrings = list(c(1,1,1,0,0,0), c(1,0)) is incorrect.
● Data Source:
BioConductor
● Keywords: internal
● Alias: buildBitString
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This is the simulator, inspired from BoolSimEngMKM in the Matlab CellNOpt, to be used on one time point simulations. Use the R interface provided by simulatorT1.
● Data Source:
BioConductor
● Keywords: internal
● Alias: cSimulator
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This function checks that all the signals in a CNOlist match to species in the model. It also checks that the CNOlist and Model lists have the right format and contain the right fields. It is called by the preprocessing function so there is no need to call it directly anymore if you use the preprocessing function.
● Data Source:
BioConductor
● Keywords:
● Alias: checkSignals
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This function compresses a model by compressing species that are not signals/inhibited/stimulated and that are not dead ends/in complex logic (i.e. only species with either one input or one output are compressed)/in self loops.
● Data Source:
BioConductor
● Keywords:
● Alias: compressModel
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providing 
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