Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)


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Documentation for package ‘hopach’ version 2.32.0

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.