Cophenetic: Compute cophenetic distances on dendrogram objects

In DECIPHER: Tools for curating, analyzing, and manipulating biological sequences

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 [e-mail]

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)

Example output

Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: RSQLite
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Time difference of 0.15 secs

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Time difference of 0.09 secs

[1] 0.9864114

DECIPHER documentation built on Nov. 8, 2020, 8:30 p.m.