hopach: Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)

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The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering).

Author
Katherine S. Pollard, with Mark J. van der Laan <laan@stat.berkeley.edu> and Greg Wall
Date of publication
None
Maintainer
Katherine S. Pollard <katherine.pollard@gladstone.ucsf.edu>
License
GPL (>= 2)
Version
2.34.0
URLs

View on Bioconductor

Man pages

boot2fuzzy
function to write MapleTree files for viewing bootstrap...
bootplot
function to make a barplot of bootstrap estimated cluster...
bootstrap
functions to perform non-parametric bootstrap resampling of...
correlationordering
function to compute empirical correlation between distance in...
disscosangle
Functions to compute pair-wise distances
distancematrix
functions to compute pair wise distances between vectors
dplot
function to make a pseudo-color image of a distance matrix...
golub
Gene expression dataset from Golub et al. (1999)
hdist-class
Class "hdist" - S4 class to hold distance matrices.
hopach
function to perform HOPACH hierarchical clustering
hopach2tree
function to write MapleTree files for viewing hopach...
hopach.internal
Functions used internally by the hopach package
labelstomss
Functions to compute silhouettes and split silhouettes
makeoutput
function to write a text file with hopach output
prune
function to prune a HOPACH tree.

Files in this package

hopach/DESCRIPTION
hopach/NAMESPACE
hopach/R
hopach/R/boot2fuzzy.R
hopach/R/bootplot.R
hopach/R/bootstrap.R
hopach/R/distance.R
hopach/R/dplot.R
hopach/R/hdistClass.R
hopach/R/hopach.R
hopach/R/hopach2tree.R
hopach/R/output.R
hopach/R/prune.R
hopach/build
hopach/build/vignette.rds
hopach/data
hopach/data/golub.RData
hopach/inst
hopach/inst/CITATION
hopach/inst/doc
hopach/inst/doc/hopach.R
hopach/inst/doc/hopach.Rnw
hopach/inst/doc/hopach.pdf
hopach/man
hopach/man/boot2fuzzy.Rd
hopach/man/bootplot.Rd
hopach/man/bootstrap.Rd
hopach/man/correlationordering.Rd
hopach/man/disscosangle.Rd
hopach/man/distancematrix.Rd
hopach/man/dplot.Rd
hopach/man/golub.Rd
hopach/man/hdist-class.Rd
hopach/man/hopach.Rd
hopach/man/hopach.internal.Rd
hopach/man/hopach2tree.Rd
hopach/man/labelstomss.Rd
hopach/man/makeoutput.Rd
hopach/man/prune.Rd
hopach/src
hopach/src/Rdistances.c
hopach/src/hdist.c
hopach/vignettes
hopach/vignettes/MSS.pdf
hopach/vignettes/bootplot.pdf
hopach/vignettes/dplot.pdf
hopach/vignettes/golub.R
hopach/vignettes/hopach.Rnw
hopach/vignettes/hopach.bib
hopach/vignettes/hopachManuscript.pdf