delta: Estimating delta values from a distance matrix.

In jingwyang/TreeExp: the R package for analyzing expression evolution based on RNA-seq data

Description

Estimating delta values from a distance matrix.

Usage

estdelta(disMat = NULL)

Arguments

disMat

a distance matrix with column and row names

Value

returns a list of two, quartet: vector of delta numbers, each corresponded to a quartet in the distance matrix. taxa: matrix of delta numbers, colnames corresponded to taxaNames taxaNames: vector of taxaNames

References

Holland,B.R. et al. 2002. Delta plots: a tool for analyzing phylogenetic distance data. Mol. Biol. Evol., 19, 2051-2059.

Examples

data(tetraExp)
dis.mat <- expdist(tetraExp, taxa = "all",
                     subtaxa = "Brain",
                     method = "pea")
deltas <- estdelta(dis.mat)
hist(deltas$quartet)

jingwyang/TreeExp documentation built on June 11, 2019, 6:17 p.m.