hopach

Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)

Bioconductor version: Development (2.8)

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 and Greg Wall

Maintainer: Katherine S. Pollard

To install this package, start R and enter:

source("http:///biocLite.R")
biocLite("hopach")    

Documentation

PDF		bootplot.pdf
PDF		dplot.pdf
PDF	R Script	hopach
PDF		hopachManuscript.pdf
PDF		MSS.pdf

Reference Manual

Details

biocViews	Clustering
Depends	R, cluster, Biobase, methods
Imports	Biobase, cluster, graphics, grDevices, methods, stats, utils
Suggests
System Requirements
License	GPL (>= 2)
URL	http://www.stat.berkeley.edu/~laan/, http://docpollard.com/
Depends On Me
Imports Me	phenoTest
Suggests Me	BiocCaseStudies
Version	2.11.0

Package Downloads

Package Source	hopach_2.11.0.tar.gz
Windows Binary	hopach_2.11.0.zip (32-bit only)
MacOS 10.5 (Leopard) binary	hopach_2.11.0.tgz
Package Downloads Report	Download Stats