CNORfuzzy: Addon to CellNOptR: Fuzzy Logic
Version 1.18.0

This package is an extension to CellNOptR. It contains additional functionality needed to simulate and train a prior knowledge network to experimental data using constrained fuzzy logic (cFL, rather than Boolean logic as is the case in CellNOptR). Additionally, this package will contain functions to use for the compilation of multiple optimization results (either Boolean or cFL).

Browse man pages Browse package API and functions Browse package files

AuthorM. Morris, T. Cokelaer
Bioconductor views Network
Date of publicationNone
MaintainerT. Cokelaer <cokelaer@ebi.ac.uk>
LicenseGPL-2
Version1.18.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CNORfuzzy")

Man pages

CNORfuzzy-package: R version of CNOFuzzy, a Constrained Fuzzy Logic Network...
CNORwrapFuzzy: CNORfuzzy analysis wrapper
compileMultiRes: Compiles results from multiple runs and produces graph for...
computeScoreFuzzy: Compute Score of a model compared to the data for a given...
defaultParametersFuzzy: Create a list of default parameters
gaDiscreteT1: Genetic algorithm used to optimise a cFL model
getRefinedModel: Refinement of Parameters of cFL model
interpretDiscreteGA: Interpreter of output of discrete genetic algorithm
plotMeanFuzzyFit: Simulates models returned from multiple cFL runs and plots...
prep4simFuzzy: Prepare a model for simulation
reduceFuzzy: Remove unnecessary interactions from cFL model
simFuzzyT1: Simulation of a cFL model
writeFuzzyNetwork: Despict the network results of training a cFL model to data...

Functions

CNORfuzzy Man page
CNORfuzzy-package Man page
CNORwrapFuzzy Man page Source code
cSimulator Source code
compileMultiRes Man page Source code
computeScoreFuzzy Man page Source code
defaultParametersFuzzy Man page Source code
fillHashTable Source code
gaDiscreteT1 Man page Source code
getEC50 Source code
getMeanFuzzy Source code
getMeanModel Source code
getNetworkInfoFuzzy Source code
getRefinedModel Man page Source code
getk Source code
hill_function Source code
interpretDiscreteGA Man page Source code
mean Source code
objFun_getEC50 Source code
plotMeanFuzzyFit Man page Source code
prep4simFuzzy Man page Source code
rSimFuzzyT1 Source code
rSimulator Source code
reduceFuzzy Man page Source code
removeRedundant Source code
shift Source code
simFuzzyT1 Man page Source code
simulate Source code
std Source code
writeFuzzyNetwork Man page Source code
writeNetworkW Source code

Files

.Rinstignore
ChangeLog
DESCRIPTION
NAMESPACE
R
R/CNORwrapFuzzy.R
R/cSimulator.R
R/compileMultiRes.R
R/computeScoreFuzzy.R
R/defaultParametersFuzzy.R
R/gaDiscreteT1.R
R/getEC50.R
R/getMeanFuzzy.R
R/getMeanModel.R
R/getRefinedModel.R
R/interpretDiscreteGA.R
R/plotMeanFuzzyFit.R
R/prep4simFuzzy.R
R/rSimFuzzyT1.R
R/rSimulator.R
R/reduceFuzzy.R
R/removeRedundant.R
R/simFuzzyT1.R
R/simulate.R
R/writeFuzzyNetwork.R
build
build/vignette.rds
inst
inst/NEWS.Rd
inst/doc
inst/doc/CNORfuzzy-vignette.R
inst/doc/CNORfuzzy-vignette.Rnw
inst/doc/CNORfuzzy-vignette.pdf
inst/unitTests
inst/unitTests/test_CNORwrapFuzzy.R
inst/unitTests/test_computeScore.R
man
man/CNORfuzzy-package.Rd
man/CNORwrapFuzzy.Rd
man/compileMultiRes.Rd
man/computeScoreFuzzy.Rd
man/defaultParametersFuzzy.Rd
man/gaDiscreteT1.Rd
man/getRefinedModel.Rd
man/interpretDiscreteGA.Rd
man/plotMeanFuzzyFit.Rd
man/prep4simFuzzy.Rd
man/reduceFuzzy.Rd
man/simFuzzyT1.Rd
man/writeFuzzyNetwork.Rd
src
src/simulatorT1.c
tests
tests/runTests.R
vignettes
vignettes/CNORfuzzy-vignette-FullAnalysis.pdf
vignettes/CNORfuzzy-vignette-FullAnalysis2.pdf
vignettes/CNORfuzzy-vignette-FullAnalysis3.pdf
vignettes/CNORfuzzy-vignette.Rnw
vignettes/README.txt
vignettes/output_dream_PKN.dot
vignettes/output_dream_PKN.png
vignettes/output_dream_PKN.sif
vignettes/output_dream_PKN.svg
vignettes/output_dream_TimesPKN.EA
vignettes/output_dream_nodesPKN.NA
vignettes/tf1.pdf
vignettes/tf2.pdf
CNORfuzzy documentation built on May 20, 2017, 10:35 p.m.