# GaGa hierarchical model for high-throughput data analysis

## Documentation for package ‘gaga’ version 2.14.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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