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 |