gaga: GaGa hierarchical model for high-throughput data analysis

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Implements the GaGa model for high-throughput data analysis, including differential expression analysis, supervised gene clustering and classification. Additionally, it performs sequential sample size calculations using the GaGa and LNNGV models (the latter from EBarrays package).

Author
David Rossell <rosselldavid@gmail.com>.
Date of publication
None
Maintainer
David Rossell <rosselldavid@gmail.com>
License
GPL (>= 2)
Version
2.20.0

View on Bioconductor

Man pages

buildPatterns
Build a matrix with all possible patterns given a number of...
checkfit
Check goodness-of-fit of GaGa and MiGaGa models
classpred
Predict the class that a new sample belongs to.
dcgamma
Approximate gamma shape distribution
findgenes
Find differentially expressed genes after GaGa or...
fitGG
Fit GaGa hierarchical model
forwsimDiffExpr
Forward simulation for differential expression.
geneclus
Cluster genes into expression patterns.
getpar
Extract hyper-parameter estimates from a gagafit or nnfit...
parest
Parameter estimates and posterior probabilities of...
plotForwSim
Plot forward simulation trajectories
posmeansGG
Gene-specific posterior means
powclasspred
Expected probability that a future sample is correctly...
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
seqBoundariesGrid
Evaluate expected utility for parametric sequential stopping...
simGG
Prior predictive simulation
simnewsamples
Posterior predictive simulation

Files in this package

gaga/ChangeLog
gaga/DESCRIPTION
gaga/NAMESPACE
gaga/R
gaga/R/buildPatterns.r
gaga/R/checkfit.gagafit.r
gaga/R/checkfit.r
gaga/R/classpred.gagafit.r
gaga/R/classpred.r
gaga/R/dcgamma.r
gaga/R/findgenes.gagafit.r
gaga/R/findgenes.matrix.r
gaga/R/findgenes.nnfit.r
gaga/R/findgenes.r
gaga/R/fitGG.r
gaga/R/fitNN.r
gaga/R/forwsimDiffExpr.r
gaga/R/geneclus.gagafit.r
gaga/R/geneclus.r
gaga/R/getpar.gagafit.r
gaga/R/getpar.r
gaga/R/groups2int.r
gaga/R/mcgamma.r
gaga/R/parest.gagafit.r
gaga/R/parest.r
gaga/R/plotForwSim.r
gaga/R/posmeansGG.gagafit.r
gaga/R/posmeansGG.r
gaga/R/powclasspred.gagafit.r
gaga/R/powclasspred.r
gaga/R/powfindgenes.r
gaga/R/powsimprior.r
gaga/R/ppGG.r
gaga/R/print.gagaclus.r
gaga/R/print.gagafit.r
gaga/R/print.gagahyp.r
gaga/R/print.nnfit.r
gaga/R/rcgamma.r
gaga/R/seqBoundariesGrid.r
gaga/R/simGG.r
gaga/R/simNN.r
gaga/R/simnewsamples.r
gaga/build
gaga/build/vignette.rds
gaga/inst
gaga/inst/CITATION
gaga/inst/doc
gaga/inst/doc/gagamanual.R
gaga/inst/doc/gagamanual.Rnw
gaga/inst/doc/gagamanual.pdf
gaga/man
gaga/man/buildPatterns.Rd
gaga/man/checkfit.Rd
gaga/man/classpred.Rd
gaga/man/dcgamma.Rd
gaga/man/findgenes.Rd
gaga/man/fitGG.Rd
gaga/man/forwsimDiffExpr.Rd
gaga/man/geneclus.Rd
gaga/man/getpar.Rd
gaga/man/parest.Rd
gaga/man/plotForwSim.Rd
gaga/man/posmeansGG.Rd
gaga/man/powclasspred.Rd
gaga/man/powfindgenes.Rd
gaga/man/print.gagaclus.Rd
gaga/man/print.gagafit.Rd
gaga/man/print.gagahyp.Rd
gaga/man/seqBoundariesGrid.Rd
gaga/man/simGG.Rd
gaga/man/simnewsamples.Rd
gaga/src
gaga/src/cseqdesma.c
gaga/src/cseqdesma.h
gaga/src/cstat.c
gaga/src/cstat.h
gaga/vignettes
gaga/vignettes/gagamanual.Rnw
gaga/vignettes/references.bib