DIRECT: Bayesian Clustering of Multivariate Data Under the Dirichlet-Process Prior
Version 1.0.1

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. .

Browse man pages Browse package API and functions Browse package files

AuthorAudrey Qiuyan Fu, Steven Russell, Sarah J. Bray and Simon Tavare
Date of publication2016-04-01 16:24:39
MaintainerAudrey Q. Fu <audreyqyfu@gmail.com>
LicenseGPL (>= 2)
Version1.0.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("DIRECT")

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

Functions

DIRECT Man page Man page Source code
DIRECT-package Man page
DPMCMC Man page Source code
arrayTSData Source code
computeClusterMean Source code
computeClusterParHastingsRatio Source code
computeCovMtx Source code
computeLogLik Source code
computeLogLikInd Source code
dDirichlet Man page Source code
dMVNorm Man page Source code
direct Man page
normalizeProbMtx Source code
outputData Man page Source code
plotClustersMean Man page Source code
plotClustersPCA Man page Source code
plotClustersSD Man page Source code
plotSimulation Man page Source code
rDirichlet Man page Source code
rMVNorm Man page Source code
reassignLabels Source code
reassignLabelsVec Source code
reflect Source code
relabel Man page Source code
resampleClusterProb Man page Source code
rmvnormpost Source code
simuDataREM Man page Source code
simuMultiClustREM Source code
simuOneClusterREM Source code
simuProcess Source code
simulateFromPrior Source code
simulateObserved Source code
simulateStocProc Source code
summaryDIRECT Man page Source code
tc.data Man page
updateClusterMemberships_MH_FRBT Source code
updateClusterMemberships_MH_Neal Source code
updateDAlpha Source code
updateIndMean Source code
updateRandomEffectsInd Source code

Files

src
src/Makevars
src/relabel_R.c
NAMESPACE
data
data/tc.data.rda
R
R/computeClusterMean.R
R/plotSimulation.R
R/simulateObserved.R
R/reflect.R
R/Dirichlet.R
R/plotClustersSD.R
R/simuDataREM.R
R/computeCovMtx.R
R/computeClusterParHastingsRatio.R
R/DIRECT.R
R/arrayTSData.R
R/relabel.R
R/updateClusterMemberships_MH_FRBT.R
R/simulateStocProc.R
R/DPMCMC.R
R/updateClusterMemberships_MH_Neal.R
R/reassignLabelsVec.R
R/simuProcess.R
R/updateIndMean.R
R/plotClustersMean.R
R/simuMultiClustREM.R
R/normalizeProbMtx.R
R/reassignLabels.R
R/updateRandomEffectsInd.R
R/simuOneClusterREM.R
R/simulateFromPrior.R
R/rmvnormpost.R
R/computeLogLik.R
R/resampleClusterProb.R
R/updateDAlpha.R
R/summaryDIRECT.R
R/computeLogLikInd.R
R/outputData.R
R/MVNorm.R
R/plotClustersPCA.R
MD5
DESCRIPTION
man
man/DPMCMC.Rd
man/plotClustersMean.Rd
man/plotClustersPCA.Rd
man/resampleClusterProb.Rd
man/summaryDIRECT.Rd
man/DIRECT-package.Rd
man/plotClustersSD.Rd
man/simuDataREM.Rd
man/outputData.Rd
man/DIRECT.Rd
man/Dirichlet.Rd
man/plotSimulation.Rd
man/MVNorm.Rd
man/tc.data.Rd
man/relabel.Rd
DIRECT documentation built on May 19, 2017, 8:08 a.m.