copheneticCoef: calculate cophenetic coefficient for a hierarchical...

In nickytong/GenAnalysis: Genomic Analysis

Description

To compute the Cophenetic Correlation Coefficient of hierarchical clustering, we need two informations: Distance matrix and Cophenetic Matrix Cophenetic Correlation Coefficient is simply correlation coefficient between distance matrix and Cophenetic matrix As the value of the Cophenetic Correlation Coefficient is quite close to 1, we can say that the clustering is quite fit. A random data would have Cophenetic Correlation Coefficient near 0.

Usage

copheneticCoef(dist, hclust)

Arguments

dist	a dist object which can be constructed by dist, ClassDiscovery::distanceMatrix, ade4::dist.binary or my binaryDist function
hclust	a hclust object returned by hclust function (either from stats::hclust or fastcluster::hclust

Value

a correlation coeficient scalar

nickytong/GenAnalysis documentation built on July 20, 2019, 8:57 a.m.