boot.exphy: Bootstrapping expression phylogeny

In jingwyang/TreeExp: 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, x, outgroup = NULL, method = c("sou", "pea",
  "spe", "euc", "cos", "jsd", "tani", "jac", "sou_v"), B = 100,
  block = 1, trees = FALSE, quiet = FALSE, rooted = is.rooted(phy),
  jumble = TRUE, mc.cores = 1)

Arguments

phy	an object of class phylo.
x	an exprssion level table: column corresponds to median expression value of all biological samples within one taxa_subtaxa group; row corresponds to othologous genes
outgroup	a vector of mode numeric or character specifying the outgroup
method	specifying which distance method to be used to estimate expression phylogeny in bootstrapping.
B	the number of bootstrap replicates.
block	the number of columns in x that will be resampled together (see details).
trees	a logical specifying whether to return the bootstrapped trees (FALSE by default).
quiet	a logical specifying whether to print more information on the screen while performing bootstrapping(FALSE by default).
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).
jumble	a logical value. By default, the rows of x are randomized to avoid artificially too large bootstrap values associated with very short branches.
mc.cores	the number of cores (CPUs) to be used (passed to parallel).

Value

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

Examples

library('ape')
data(tetraExp)
dismat <- expdist(tetraExp, taxa = "all",
                 subtaxa = "Brain",
                 method = "pea")
tr <- root(NJ(dismat), "Chicken_Brain", resolve.root = TRUE)
plot(tr)
exp_table <- exptabTE(tetraExp, taxa = "all", subtaxa = "Brain")
bs <- boot.exphy(phy = tr, x = exp_table, method = "sou",
                 B = 100, outgroup = "Chicken_Brain")
nodelabels(bs)

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