Cophenetic {DECIPHER}R Documentation

Compute cophenetic distances on dendrogram objects

Description

Calculates the matrix of cophenetic distances represented by a dendrogram object.

Usage

Cophenetic(x)

Arguments

x

A dendrogram object.

Details

The cophenetic distance between two observations is defined as the branch length separating them on a dendrogram. This function differs from the cophenetic function in that it does not assume the tree is ultrametric and outputs the branch length separating pairs of observations rather than the height of their merger. A dendrogram that better preserves a distance matrix will show higher correlation between the distance matrix and it cophenetic distances.

Value

An object of class 'dist'.

Author(s)

Erik Wright eswright@pitt.edu

See Also

IdClusters

Examples

fas <- system.file("extdata", "Bacteria_175seqs.fas", package="DECIPHER")
dna <- readDNAStringSet(fas)
d1 <- DistanceMatrix(dna, type="dist")
dend <- IdClusters(d1, method="NJ", type="dendrogram")
d2 <- Cophenetic(dend)
cor(d1, d2)

[Package DECIPHER version 2.18.1 Index]