expdist: Expression distance matrix generated from a 'taxaExp' object

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

Description

Generate an expression distance matrix from an object of taxaExp class using a specified distance method

Usage

expdist(objects = NULL, taxa = "all", subtaxa = "all",
  rowindex = NULL, method = c("sou", "sou_v", "pea", "spe", "euc",
  "cos", "jsd", "tani", "jac"), logrithm = TRUE)

Arguments

objects	a vector of objects of class taxonExp or an object of class taxaExp
taxa	one single character or a vector of characters specifying main taxa selected for calculating expression distance. If one single character "all" is given, all the taxa included in the taxaExp will be matched and selected ("all" by default).
subtaxa	one single character or a vector of characters sepcifying sub taxa selected for calculating expression distance. If one singke character "all" is given, all the subtaxa included in the taxaExp will be matched and selected ("all" by default).
rowindex	a vector of numbers corresponded to indices of selecting rows
method	specifying which distance method to be used to estimate expression phylogeny in bootstrapping.
logrithm	a logical specifying whether to apply expression value log2 tranformation (TRUE by default).

Value

returns an expression distance matrix

Examples

data(tetraExp)
library('ape')
dismat <- expdist(tetraExp, taxa = "all",
                 subtaxa = "Brain",
                 method = "pea")
tr <- root(NJ(dismat), "Chicken_Brain")
plot(tr)

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