getAllClusters: Generate a list of all possible clusters from a hierarchical...

In uc-bd2k/gimmR: This package was built to cluster gene expression data using the Gaussian Infinite Mixture Model.

Description

The function take an hclust object and returns a list of all possible clusters of desired minimum to maximum size. Clusters are determined by cutting the tree at a given level and recording the leaf node labels of the resulting subtree(s).

Usage

getAllClusters(tree, maxSize = 1000, minSize = 10, clusterList = NULL, k=NULL)

Arguments

tree	a hierarchical clustering (hclust object)
maxSize	maximum cluster size
minSize	minimum cluster size
clusterList	depricated. kept for backward compatibilty.
k	Maximum number of clusters. If specified, the list of clusters will be restricted to the top k clusters within the minSize-maxSize range starting at the root.

Value

A list where each list element is a vector of leaf nodes described by the labels slot of the original tree (hclust object).

Author(s)

Johannes Freudenberg

See Also

hclust

Examples

gtr <- hclust(dist(1:10))
gtr$labels <- 1:10
plot(gtr)
getAllClusters(gtr, 10, 2)

uc-bd2k/gimmR documentation built on May 3, 2019, 2:15 p.m.