BHC: Bayesian Hierarchical Clustering
Version 1.28.0

The method performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge. This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) or time-series data. This version also includes a randomised algorithm which is more efficient for larger data sets.

AuthorRich Savage, Emma Cooke, Robert Darkins, Yang Xu
Bioconductor views Clustering Microarray
Date of publicationNone
MaintainerRich Savage <r.s.savage@warwick.ac.uk>
LicenseGPL-3
Version1.28.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("BHC")

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Man pages

BHC: Function to perform Bayesian Hierarchical Clustering on a 2D...

Functions

ConstructDendrogramObject Source code
DiscretiseData Man page Source code
FindOptimalBinning Man page Source code
FindOptimalHyperparameter Source code
RunBhcWrapper Source code
WriteOutClusterLabels Man page Source code
bhc Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/ConstructDendrogramObject.R
R/DiscretiseData.R
R/FindOptimalBinning.R
R/FindOptimalHyperparameter.R
R/RunBhcWrapper.R
R/WriteOutClusterLabels.R
R/bhc.R
build
build/vignette.rds
configure
configure.ac
inst
inst/doc
inst/doc/bhc.R
inst/doc/bhc.Rnw
inst/doc/bhc.pdf
man
man/BHC.Rd
src
src/BlockCovarianceMatrix.cpp
src/BlockCovarianceMatrix.h
src/CubicSplineTimecourseDataSet.cpp
src/CubicSplineTimecourseDataSet.h
src/DataSet.cpp
src/DataSet.h
src/DirichletProcessMixture.cpp
src/DirichletProcessMixture.h
src/Makevars
src/Makevars.in
src/MultinomialDataSet.cpp
src/MultinomialDataSet.h
src/Node.cpp
src/Node.h
src/RobustCubicSplineTimecourseDataSet.cpp
src/RobustCubicSplineTimecourseDataSet.h
src/RobustSquaredExponentialTimecourseDataSet.cpp
src/RobustSquaredExponentialTimecourseDataSet.h
src/SquaredExponentialTimecourseDataSet.cpp
src/SquaredExponentialTimecourseDataSet.h
src/TimecourseDataSet.cpp
src/TimecourseDataSet.h
src/bhc.cpp
src/gammaln.cpp
src/gammaln.h
src/header.cpp
src/header.h
src/multinomial_CalculateHyperparameters.cpp
src/multinomial_OutputDendrogramInformation.cpp
src/multinomial_ReadInData.cpp
src/multinomial_bayeslink_binf.cpp
src/multinomial_binevidence.cpp
src/multinomial_header.h
vignettes
vignettes/bhc.Rnw
BHC documentation built on May 20, 2017, 10:17 p.m.

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