| 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 |