hopach

Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)

Bioconductor version: 2.5

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 at stat.berkeley.edu> and Greg Wall

Maintainer: Katherine S. Pollard <katherine.pollard at gladstone.ucsf.edu>

To install this package, start R and enter:

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

To cite this package in a publication, start R and enter:

    citation("hopach")

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