boot.exphy: Bootstrapping expression phylogeny

In HangRuan1912/phyExp: the R package for analyzing expression evolution based on RNA-seq data

Description

bootstrap by resampling gene (gene, transcript, exon, etc..)

Usage

boot.exphy(phy = NULL, objects = NULL, rowindex = NULL,
  method = c("sou", "pea", "spe", "euc", "cos", "jsd", "tani", "jac", "u",
  "nbdln"), B = 100, rooted = NULL, trees = FALSE)

Arguments

phy	an object of class phylo.
objects	a vector of objects of class taxonExp or an object of class taxaExp.
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.
B	the number of bootstrap replicates.
rooted	if "phy" is a rooted tree, a character of the root node's label when constructing "phy"; if "phy" is unrooted tree, NULL (NULL by default).
trees	a logical specifying whether to return the bootstrapped trees (FALSE by default).

Value

similar to boot.phylo in ape, boot.exptree returns a numeric vector which ith element is the number associated to the ith node of phy. if trees = TRUE, boot.exptree returns a list whose first element (named "BP") is like before, and the second element("trees") is a list with the bootstrapped trees.

Author(s)

Hang Ruan ([e-mail]).

Examples

data(tetraexp)
dismat <- expdist(tetraexp.objects, taxa = "all",
                 subtaxa = "Brain",
                 method = "pea")
tr <- root(NJ(dismat), "Chicken_Brain")
plot(tr)
bs <- boot.exphy(tr, tetraexp.objects, method = "sou",
                 B = 100, rooted = "Chicken_Brain")
nodelabels(bs)

HangRuan1912/phyExp documentation built on July 15, 2019, 9:01 p.m.