Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)

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Documentation for package ‘hopach’ version 2.62.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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