Ternary Network Estimation


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Documentation for package ‘ternarynet’ version 1.40.0

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A B C D E F G I M N P R S T X

-- A --

attractorSummary Summarize Attractors

-- B --

backupStage Ternary Network Fitting Parameters
backupStage-method Ternary Network Fitting Parameters
backupStage<- Ternary Network Fitting Parameters
backupStage<--method Ternary Network Fitting Parameters
beta0 Ternary Network Fitting Parameters
beta0-method Ternary Network Fitting Parameters
beta0<- Ternary Network Fitting Parameters
beta0<--method Ternary Network Fitting Parameters

-- C --

chi0 Ternary Network Fitting Parameters
chi0-method Ternary Network Fitting Parameters
chi0<- Ternary Network Fitting Parameters
chi0<--method Ternary Network Fitting Parameters
class:ternaryFit Ternary Network Fit
class:ternaryFitParameters Ternary Network Fitting Parameters
class:ternaryPost Ternary Network Posterior

-- D --

degreeObjMin Ternary Network Fit
degreeObjMin-method Ternary Network Fit
degreeObjMin<- Ternary Network Fit
degreeObjMin<--method Ternary Network Fit
degreeObjs Ternary Network Posterior
degreeObjs-method Ternary Network Posterior
degreeObjs<- Ternary Network Posterior
degreeObjs<--method Ternary Network Posterior
delta Ternary Network Fitting Parameters
delta-method Ternary Network Fitting Parameters
delta<- Ternary Network Fitting Parameters
delta<--method Ternary Network Fitting Parameters
dim-method Ternary Network Fit
dim-method Ternary Network Posterior

-- E --

edgePenalty Ternary Network Fitting Parameters
edgePenalty-method Ternary Network Fitting Parameters
edgePenalty<- Ternary Network Fitting Parameters
edgePenalty<--method Ternary Network Fitting Parameters
epsilon Ternary Network Fitting Parameters
epsilon-method Ternary Network Fitting Parameters
epsilon<- Ternary Network Fitting Parameters
epsilon<--method Ternary Network Fitting Parameters
experimentNames Ternary Network Fit
experimentNames-method Ternary Network Fit
experimentNames-method Ternary Network Posterior
experimentNames<- Ternary Network Fit
experimentNames<--method Ternary Network Fit
experimentNames<--method Ternary Network Posterior

-- F --

finalTemperature Ternary Network Fit
finalTemperature-method Ternary Network Fit
finalTemperature<- Ternary Network Fit
finalTemperature<--method Ternary Network Fit

-- G --

geneNames Ternary Network Fit
geneNames-method Ternary Network Fit
geneNames-method Ternary Network Posterior
geneNames<- Ternary Network Fit
geneNames<--method Ternary Network Fit
geneNames<--method Ternary Network Posterior
graphObjMin Ternary Network Fit
graphObjMin-method Ternary Network Fit
graphObjMin<- Ternary Network Fit
graphObjMin<--method Ternary Network Fit
graphObjs Ternary Network Posterior
graphObjs-method Ternary Network Posterior
graphObjs<- Ternary Network Posterior
graphObjs<--method Ternary Network Posterior
graphPosterior Network Topology

-- I --

initialize-method Ternary Network Fit
initialize-method Ternary Network Fitting Parameters
initialize-method Ternary Network Posterior
inputParams Ternary Network Fit
inputParams-method Ternary Network Fit
inputParams-method Ternary Network Posterior
inputParams<- Ternary Network Fit
inputParams<--method Ternary Network Fit
inputParams<--method Ternary Network Posterior

-- M --

m0 Ternary Network Fitting Parameters
m0-method Ternary Network Fitting Parameters
m0<- Ternary Network Fitting Parameters
m0<--method Ternary Network Fitting Parameters
maxDegree Ternary Network Fitting Parameters
maxDegree-method Ternary Network Fitting Parameters
maxDegree<- Ternary Network Fitting Parameters
maxDegree<--method Ternary Network Fitting Parameters
maxStage Ternary Network Fitting Parameters
maxStage-method Ternary Network Fitting Parameters
maxStage<- Ternary Network Fitting Parameters
maxStage<--method Ternary Network Fitting Parameters
maxTransition Ternary Network Fitting Parameters
maxTransition-method Ternary Network Fitting Parameters
maxTransition<- Ternary Network Fitting Parameters
maxTransition<--method Ternary Network Fitting Parameters
minScore Ternary Network Fit
minScore-method Ternary Network Fit
minScore<- Ternary Network Fit
minScore<--method Ternary Network Fit

-- N --

ne Ternary Network Fitting Parameters
ne-method Ternary Network Fitting Parameters
ne<- Ternary Network Fitting Parameters
ne<--method Ternary Network Fitting Parameters
neighborDegree Ternary Network Fitting Parameters
neighborDegree-method Ternary Network Fitting Parameters
neighborDegree<- Ternary Network Fitting Parameters
neighborDegree<--method Ternary Network Fitting Parameters
newScore Ternary Network Fit
newScore-method Ternary Network Fit
newScore<- Ternary Network Fit
newScore<--method Ternary Network Fit

-- P --

pAddParent Ternary Network Fitting Parameters
pAddParent-method Ternary Network Fitting Parameters
pAddParent<- Ternary Network Fitting Parameters
pAddParent<--method Ternary Network Fitting Parameters
parallelFit Fit ternary network models using parallel tempering
perturbationObj Ternary Network Fit
perturbationObj-method Ternary Network Fit
perturbationObj-method Ternary Network Posterior
perturbationObj<- Ternary Network Fit
perturbationObj<--method Ternary Network Fit
perturbationObj<--method Ternary Network Posterior
perturbationType Ternary Network Fitting Parameters
perturbationType-method Ternary Network Fitting Parameters
perturbationType<- Ternary Network Fitting Parameters
perturbationType<--method Ternary Network Fitting Parameters
pExchangeParent Ternary Network Fitting Parameters
pExchangeParent-method Ternary Network Fitting Parameters
pExchangeParent<- Ternary Network Fitting Parameters
pExchangeParent<--method Ternary Network Fitting Parameters
plotFit Network Fit Plot
plotPost Network Posterior Plot
plotTraces Network Fit Traces
pNeighborhood Ternary Network Fitting Parameters
pNeighborhood-method Ternary Network Fitting Parameters
pNeighborhood<- Ternary Network Fitting Parameters
pNeighborhood<--method Ternary Network Fitting Parameters
predictAttractor Predict the attractor(s) resulting from a given perturbation

-- R --

rho Ternary Network Fitting Parameters
rho-method Ternary Network Fitting Parameters
rho<- Ternary Network Fitting Parameters
rho<--method Ternary Network Fitting Parameters

-- S --

scores Ternary Network Posterior
scores-method Ternary Network Posterior
scores<- Ternary Network Posterior
scores<--method Ternary Network Posterior
scoreType Ternary Network Fitting Parameters
scoreType-method Ternary Network Fitting Parameters
scoreType<- Ternary Network Fitting Parameters
scoreType<--method Ternary Network Fitting Parameters
show-method Ternary Network Fit
show-method Ternary Network Fitting Parameters
show-method Ternary Network Posterior
simulateSteadyState Simulate Steady State Data
stageCount Ternary Network Fit
stageCount-method Ternary Network Fit
stageCount<- Ternary Network Fit
stageCount<--method Ternary Network Fit
steadyStateObj Ternary Network Fit
steadyStateObj-method Ternary Network Fit
steadyStateObj-method Ternary Network Posterior
steadyStateObj<- Ternary Network Fit
steadyStateObj<--method Ternary Network Fit
steadyStateObj<--method Ternary Network Posterior

-- T --

tableObjMin Ternary Network Fit
tableObjMin-method Ternary Network Fit
tableObjMin<- Ternary Network Fit
tableObjMin<--method Ternary Network Fit
tableObjs Ternary Network Posterior
tableObjs-method Ternary Network Posterior
tableObjs<- Ternary Network Posterior
tableObjs<--method Ternary Network Posterior
ternaryFit Ternary Network Fit
ternaryFit-class Ternary Network Fit
ternaryFit-methods Ternary Network Fit
ternaryFitParameters Ternary Network Fitting Parameters
ternaryFitParameters-class Ternary Network Fitting Parameters
ternaryFitParameters-methods Ternary Network Fitting Parameters
ternaryPost Ternary Network Posterior
ternaryPost-class Ternary Network Posterior
ternaryPost-methods Ternary Network Posterior
tnetfit Ternary Network Fitting
tnetpost Ternary Network Posterior Sampling
traces Ternary Network Fit
traces-method Ternary Network Fit
traces<- Ternary Network Fit
traces<--method Ternary Network Fit

-- X --

xSeed Ternary Network Fit
xSeed-method Ternary Network Fit
xSeed<- Ternary Network Fit
xSeed<--method Ternary Network Fit