GaGa hierarchical model for high-throughput data analysis

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Documentation for package ‘gaga’ version 2.34.0

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adjustfitNN Fit GaGa hierarchical model
buildPatterns Build a matrix with all possible patterns given a number of groups where samples may belong to.
checkfit Check goodness-of-fit of GaGa and MiGaGa models
checkfit.gagafit Check goodness-of-fit of GaGa and MiGaGa models
classpred Predict the class that a new sample belongs to.
classpred.gagafit Predict the class that a new sample belongs to.
dcgamma Approximate gamma shape distribution
findgenes Find differentially expressed genes after GaGa or Normal-Normal fit.
findgenes.gagafit Find differentially expressed genes after GaGa or Normal-Normal fit.
findgenes.nnfit Find differentially expressed genes after GaGa or Normal-Normal fit.
fitGG Fit GaGa hierarchical model
fitNN Fit GaGa hierarchical model
fitNNSingleHyp Fit GaGa hierarchical model
forwsimDiffExpr Forward simulation for differential expression.
forwsimDiffExpr.gagafit Forward simulation for differential expression.
forwsimDiffExpr.nnfit Forward simulation for differential expression.
geneclus Cluster genes into expression patterns.
geneclus.gagafit Cluster genes into expression patterns.
getpar Extract hyper-parameter estimates from a gagafit or nnfit object
getpar.gagafit Extract hyper-parameter estimates from a gagafit or nnfit object
getpar.nnfit Extract hyper-parameter estimates from a gagafit or nnfit object
mcgamma Approximate gamma shape distribution
parest Parameter estimates and posterior probabilities of differential expression for GaGa and MiGaGa model
parest.gagafit Parameter estimates and posterior probabilities of differential expression for GaGa and MiGaGa model
plotForwSim Plot forward simulation trajectories
posmeansGG Gene-specific posterior means
posmeansGG.gagafit Gene-specific posterior means
powclasspred Expected probability that a future sample is correctly classified.
powclasspred.gagafit Expected probability that a future sample is correctly classified.
powfindgenes Power computations for differential expression
print.gagaclus Print an object of class gagaclus
print.gagafit Print an object of class gagafit or nnfit
print.gagahyp Print an object of class gagahyp
print.nnfit Print an object of class gagafit or nnfit
rcgamma Approximate gamma shape distribution
seqBoundariesGrid Evaluate expected utility for parametric sequential stopping boundaries.
simGG Prior predictive simulation
simLNN Prior predictive simulation
simnewsamples Posterior predictive simulation
simnewsamples.gagafit Posterior predictive simulation
simnewsamples.nnfit Posterior predictive simulation
simNN Prior predictive simulation