hopach: Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)
Version 2.36.0

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).

Browse man pages Browse package API and functions Browse package files

AuthorKatherine S. Pollard, with Mark J. van der Laan <laan@stat.berkeley.edu> and Greg Wall
Bioconductor views Clustering
Date of publicationNone
MaintainerKatherine S. Pollard <katherine.pollard@gladstone.ucsf.edu>
LicenseGPL (>= 2)
Version2.36.0
URL http://www.stat.berkeley.edu/~laan/ http://docpollard.org/
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("hopach")

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.

Functions

[,hdist-method Man page
as.hdist Man page Source code
as.hdist,matrix-method Man page
as.matrix,hdist-method Man page
as.vector,hdist,missing-method Man page
as.vector,hdist-method Man page
boot2fuzzy Man page Source code
boothopach Man page Source code
bootmedoids Man page Source code
bootplot Man page Source code
coerce,hdist,matrix-method Man page
coerce,matrix,hdist-method Man page
collap Man page Source code
correlationordering Man page Source code
cutdigits Man page Source code
cutzeros Man page Source code
digits Man page Source code
dim,hdist-method Man page
dissabscor Man page Source code
dissabscosangle Man page Source code
disscor Man page Source code
disscosangle Man page Source code
disseuclid Man page Source code
dissmatrix Man page Source code
dissvector Man page Source code
distancematrix Man page Source code
distancevector Man page Source code
dplot Man page Source code
generic,as.vector,hdist-method Man page
golub Man page
golub.cl Man page
golub.gnames Man page
hdist Man page
hdist-class Man page
hopach Man page Source code
hopach2tree Man page Source code
improveordering Man page Source code
is.hdist Man page
labels,hdist-method Man page
labelstomss Man page Source code
length,hdist-method Man page
makeTree Man page Source code
makeoutput Man page Source code
msscheck Man page Source code
msscollap Man page Source code
msscomplete Man page Source code
mssinitlevel Man page Source code
mssmulticollap Man page Source code
mssnextlevel Man page Source code
mssrundown Man page Source code
msssplitcluster Man page Source code
newnextlevel Man page Source code
newsplitcluster Man page Source code
nonzeros Man page Source code
orderelements Man page Source code
paircoll Man page Source code
print.hdist Source code
prune Man page Source code
show,hdist-method Man page
silcheck Man page Source code
vdissabscor Man page Source code
vdissabscosangle Man page Source code
vdissabseuclid Man page Source code
vdisscor Man page Source code
vdisscosangle Man page Source code
vdisseuclid Man page Source code
vectmatrix Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/boot2fuzzy.R
R/bootplot.R
R/bootstrap.R
R/distance.R
R/dplot.R
R/hdistClass.R
R/hopach.R
R/hopach2tree.R
R/output.R
R/prune.R
build
build/vignette.rds
data
data/golub.RData
inst
inst/CITATION
inst/doc
inst/doc/hopach.R
inst/doc/hopach.Rnw
inst/doc/hopach.pdf
man
man/boot2fuzzy.Rd
man/bootplot.Rd
man/bootstrap.Rd
man/correlationordering.Rd
man/disscosangle.Rd
man/distancematrix.Rd
man/dplot.Rd
man/golub.Rd
man/hdist-class.Rd
man/hopach.Rd
man/hopach.internal.Rd
man/hopach2tree.Rd
man/labelstomss.Rd
man/makeoutput.Rd
man/prune.Rd
src
src/Rdistances.c
src/hdist.c
vignettes
vignettes/MSS.pdf
vignettes/bootplot.pdf
vignettes/dplot.pdf
vignettes/golub.R
vignettes/hopach.Rnw
vignettes/hopach.bib
vignettes/hopachManuscript.pdf
hopach documentation built on May 20, 2017, 10:03 p.m.