Package: hopach 2.67.0

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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hopach.pdf |hopach.html✨
hopach/json (API)

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

Peer review:

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-2.67.0(bioc 3.21)hopach-2.66.0(bioc 3.20)

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

clustering

6.05 score 5 packages 53 scripts 598 downloads 7 mentions 53 exports 4 dependencies

Last updated 2 months agofrom:1e519496ab. Checks:OK: 9. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-win-x86_64OKNov 29 2024
R-4.5-linux-x86_64OKNov 29 2024
R-4.4-win-x86_64OKNov 29 2024
R-4.4-mac-x86_64OKNov 29 2024
R-4.4-mac-aarch64OKNov 29 2024
R-4.3-win-x86_64OKNov 29 2024
R-4.3-mac-x86_64OKNov 29 2024
R-4.3-mac-aarch64OKNov 29 2024

Exports:as.hdistas.matrixboot2fuzzyboothopachbootmedoidsbootplotcoercecollapcorrelationorderingcutdigitscutzerosdigitsdissabscordissabscosangledisscordisscosangledisseucliddissmatrixdissvectordistancematrixdistancevectordplothdisthopachhopach2treeimproveorderingis.hdistlabelstomssmakeoutputmakeTreemsscheckmsscollapmsscompletemssinitlevelmssmulticollapmssnextlevelmssrundownmsssplitclusternewnextlevelnewsplitclusternonzerosorderelementspaircollpruneshowsilcheckvdissabscorvdissabscosanglevdissabseuclidvdisscorvdisscosanglevdisseuclidvectmatrix

Dependencies:BiobaseBiocGenericsclustergenerics

hopach

Rendered fromhopach.Rnwusingutils::Sweaveon Nov 29 2024.

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

Readme and manuals

Help Manual

Help pageTopics
function to write MapleTree files for viewing bootstrap estimated cluster membership probabilities based on hopach clustering resultsboot2fuzzy
functions to perform non-parametric bootstrap resampling of hopach clustering resultsboothopach bootmedoids
function to make a barplot of bootstrap estimated cluster membership probabilitiesbootplot
function to compute empirical correlation between distance in a list and distance by a metriccorrelationordering improveordering
functions to compute pair wise distances between vectorsdissmatrix 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 clusteringhopach
function to write MapleTree files for viewing hopach hierarchical clustering resultshopach2tree makeTree
Functions to compute silhouettes and split silhouetteslabelstomss msscheck silcheck
function to write a text file with hopach outputmakeoutput
function to prune a HOPACH tree.prune