GaGa hierarchical model for high-throughput data analysis


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Documentation for package ‘gaga’ version 2.0.0

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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 fit.
findgenes.gagafit Find differentially expressed genes after GaGa fit.
fitGG Fit GaGa hierarchical model
forwsimDiffExpr 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 object
getpar.gagafit Extract hyper-parameter estimates from a gagafit 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
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
print.gagahyp Print an object of class gagahyp
rcgamma Approximate gamma shape distribution
seqBoundariesGrid Evaluate expected utility for parametric sequential stopping boundaries.
simGG Prior predictive simulation
simnewsamples Posterior predictive simulation
simnewsamples.gagafit Posterior predictive simulation