tool.cluster.static: Static hierarchical clustering

In Mergeomics: Integrative network analysis of omics data

Description

tool.cluster.static takes dendrogram (clustering tree) and its cutting height; then, obtains cluster labels for the nodes of the tree.

Usage

tool.cluster.static(dendro, hlim)

Arguments

dendro	dendrogram (tree)
hlim	cutting height of the dendrogram

Value

clusters

cluster labels of the components after static clustering

Author(s)

Ville-Petteri Makinen

References

Shu L, Zhao Y, Kurt Z, Byars SG, Tukiainen T, Kettunen J, Orozco LD, Pellegrini M, Lusis AJ, Ripatti S, Zhang B, Inouye M, Makinen V-P, Yang X. Mergeomics: multidimensional data integration to identify pathogenic perturbations to biological systems. BMC genomics. 2016;17(1):874.

Examples

set.seed(1)
## assume that we have a dataset including several samples 
## with distinct features
dataset <- matrix(rnorm(20), ncol=5) ## 4 samples with 5 features
## Find the distances between each sample pair to cluster them
d <- dist(dataset, method = "euclidean", upper=TRUE, diag=TRUE)
tree <- hclust(d)
## Height cutoff.
hlim <- max(tree$height)
## Find clusters.
clusters <- tool.cluster.static(tree, hlim)

Mergeomics documentation built on Nov. 8, 2020, 6:58 p.m.