Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

CellNOptR

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

This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network.

Functions (90)

CNORbool

Simple Boolean analysis standalone

CNORwrap

CNOR analysis wrapper

CNOdata

Get data from a CellNOpt data repository

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

CNOlistToyMMB

Toy data

CellNOptR-package

R version of CellNOptR, boolean features

DreamModel

Model used for the DREAM3 challenge

ToyModel

Toy model

ToyModel2

Toy model

buildBitString

Build the final bit string vector and times vector based on a list of optimised bit strings at different time points.

build_sif_table_from_rule

Build a SIF table from a logic rule written in a string

cSimulator

C-implementation of simulatorT1.

checkSignals

Check the CNOlist and model matching

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

defaultParameters

Create a list of default parameters

exhaustive

Exhaustive search over the optimisation of a PKN model on MIDAS data.

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

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.

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

normaliseCNOlist

Normalisation for boolean modelling.

plot-methods

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