DIRECT: Bayesian Clustering of Multivariate Data Under the Dirichlet-Process Prior

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A Bayesian clustering method for replicated time series or replicated measurements from multiple experimental conditions, e.g., time-course gene expression data. It estimates the number of clusters directly from the data using a Dirichlet-process prior. See Fu, A. Q., Russell, S., Bray, S. and Tavare, S. (2013) Bayesian clustering of replicated time-course gene expression data with weak signals. The Annals of Applied Statistics. 7(3) 1334-1361. <doi:10.1214/13-AOAS650>.

Author
Audrey Qiuyan Fu, Steven Russell, Sarah J. Bray and Simon Tavare
Date of publication
2016-04-01 16:24:39
Maintainer
Audrey Q. Fu <audreyqyfu@gmail.com>
License
GPL (>= 2)
Version
1.0.1

View on CRAN

Man pages

DIRECT
Bayesian Clustering with the Dirichlet-Process Prior
DIRECT-package
Bayesian Clustering of Multivariate Data with the...
Dirichlet
The Dirichlet Distribution
DPMCMC
Dirichlet Process-Based Markov Chain Monte Carlo (MCMC)...
MVNorm
The Multivariate Normal Distribution
outputData
Writing Simulation Parameters and Data to Files
plotClustersMean
Plotting Clustered Mean Vectors
plotClustersPCA
PCA Plot for Posterior Allocation Probability Matrix
plotClustersSD
Plotting Posterior Estimates of Cluster-Specific Random...
plotSimulation
Plotting Data Simulated Under A Random-Effects Mixture Model
relabel
A Relabel Algorithm
resampleClusterProb
Resampling to Estimate Posterior Allocation Probability...
simuDataREM
Data Simulation Under the Random-Effects Mixture Model
summaryDIRECT
Processing Posterior Estimates for Clustering Under DIRECT
tc.data
Time-Course Microarray Gene Expression Data

Files in this package

DIRECT
DIRECT/src
DIRECT/src/Makevars
DIRECT/src/relabel_R.c
DIRECT/NAMESPACE
DIRECT/data
DIRECT/data/tc.data.rda
DIRECT/R
DIRECT/R/computeClusterMean.R
DIRECT/R/plotSimulation.R
DIRECT/R/simulateObserved.R
DIRECT/R/reflect.R
DIRECT/R/Dirichlet.R
DIRECT/R/plotClustersSD.R
DIRECT/R/simuDataREM.R
DIRECT/R/computeCovMtx.R
DIRECT/R/computeClusterParHastingsRatio.R
DIRECT/R/DIRECT.R
DIRECT/R/arrayTSData.R
DIRECT/R/relabel.R
DIRECT/R/updateClusterMemberships_MH_FRBT.R
DIRECT/R/simulateStocProc.R
DIRECT/R/DPMCMC.R
DIRECT/R/updateClusterMemberships_MH_Neal.R
DIRECT/R/reassignLabelsVec.R
DIRECT/R/simuProcess.R
DIRECT/R/updateIndMean.R
DIRECT/R/plotClustersMean.R
DIRECT/R/simuMultiClustREM.R
DIRECT/R/normalizeProbMtx.R
DIRECT/R/reassignLabels.R
DIRECT/R/updateRandomEffectsInd.R
DIRECT/R/simuOneClusterREM.R
DIRECT/R/simulateFromPrior.R
DIRECT/R/rmvnormpost.R
DIRECT/R/computeLogLik.R
DIRECT/R/resampleClusterProb.R
DIRECT/R/updateDAlpha.R
DIRECT/R/summaryDIRECT.R
DIRECT/R/computeLogLikInd.R
DIRECT/R/outputData.R
DIRECT/R/MVNorm.R
DIRECT/R/plotClustersPCA.R
DIRECT/MD5
DIRECT/DESCRIPTION
DIRECT/man
DIRECT/man/DPMCMC.Rd
DIRECT/man/plotClustersMean.Rd
DIRECT/man/plotClustersPCA.Rd
DIRECT/man/resampleClusterProb.Rd
DIRECT/man/summaryDIRECT.Rd
DIRECT/man/DIRECT-package.Rd
DIRECT/man/plotClustersSD.Rd
DIRECT/man/simuDataREM.Rd
DIRECT/man/outputData.Rd
DIRECT/man/DIRECT.Rd
DIRECT/man/Dirichlet.Rd
DIRECT/man/plotSimulation.Rd
DIRECT/man/MVNorm.Rd
DIRECT/man/tc.data.Rd
DIRECT/man/relabel.Rd