Package: hopach 2.73.0

Katherine S. Pollard

hopach: Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)

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).

Authors:Katherine S. Pollard, with Mark J. van der Laan <[email protected]> and Greg Wall

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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
hopach/json (API)

# Install 'hopach' in R:

install.packages('hopach', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Datasets:

golub - Gene expression dataset from Golub et al.
golub.cl - Gene expression dataset from Golub et al.
golub.gnames - Gene expression dataset from Golub et al.

On BioConductor:hopach-2.73.0(bioc 3.24)hopach-2.72.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

clustering

6.10 score 5 packages 60 scripts 7 mentions 53 exports 4 dependencies

Last updated from:6f6ebe8ff3. Checks:1 ERROR, 13 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	145
linux-devel-arm64	OK	142
linux-devel-x86_64	OK	157
source / vignettes	OK	174
linux-release-arm64	OK	153
linux-release-x86_64	OK	126
macos-release-arm64	OK	99
macos-release-x86_64	OK	272
macos-oldrel-arm64	OK	110
macos-oldrel-x86_64	OK	246
windows-devel	OK	119
windows-release	OK	108
windows-oldrel	OK	109
wasm-release	OK	100

Exports:as.hdist as.matrix boot2fuzzy boothopach bootmedoids bootplot coerce collap correlationordering cutdigits cutzeros digits dissabscor dissabscosangle disscor disscosangle disseuclid dissmatrix dissvector distancematrix distancevector dplot hdist hopach hopach2tree improveordering is.hdist labelstomss makeoutput makeTree msscheck msscollap msscomplete mssinitlevel mssmulticollap mssnextlevel mssrundown msssplitcluster newnextlevel newsplitcluster nonzeros orderelements paircoll prune show silcheck vdissabscor vdissabscosangle vdissabseuclid vdisscor vdisscosangle vdisseuclid vectmatrix

Dependencies:Biobase BiocGenerics cluster generics

hopach

Rendered fromhopach.Rnwusingutils::Sweave

Last update: 2013-11-01
Started: 2013-11-01

Help page	Topics
function to write MapleTree files for viewing bootstrap estimated cluster membership probabilities based on hopach clustering results	boot2fuzzy
functions to perform non-parametric bootstrap resampling of hopach clustering results	boothopach bootmedoids
function to make a barplot of bootstrap estimated cluster membership probabilities	bootplot
function to compute empirical correlation between distance in a list and distance by a metric	correlationordering improveordering
functions to compute pair wise distances between vectors	dissmatrix dissvector distancematrix distancevector vectmatrix
function to make a pseudo-color image of a distance matrix with the row and column ordering based on HOPACH clustering results.	dplot
Gene expression dataset from Golub et al. (1999)	golub golub.cl golub.gnames
Class "hdist" - S4 class to hold distance matrices.	as.hdist as.hdist,matrix-method as.matrix,hdist-method as.vector,hdist,missing-method as.vector,hdist-method coerce,hdist,matrix-method coerce,matrix,hdist-method dim,hdist-method generic,as.vector,hdist-method hdist hdist-class is.hdist labels,hdist-method length,hdist-method show,hdist-method [,hdist-method
function to perform HOPACH hierarchical clustering	hopach
function to write MapleTree files for viewing hopach hierarchical clustering results	hopach2tree makeTree
Functions to compute silhouettes and split silhouettes	labelstomss msscheck silcheck
function to write a text file with hopach output	makeoutput
function to prune a HOPACH tree.	prune

Package: hopach 2.73.0

hopach: Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)

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