# Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)

## Documentation for package ‘hopach’ version 2.12.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## 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.
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.