gamma: Estimating gamma from taxaExp objects.

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

Description

Estimating gamma from taxaExp objects.

Usage

estgamma(objects = NULL, taxa = NULL, subtaxa = NULL,
  method = c("sou", "ced", "pea", "souln", "nbdln", "euc", "cos", "jsd"))

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 gammaD and gammaE. 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 gammaD and gammaE. #' If one single character "all" is given, all the taxa included in the taxaExp will be matched and selected ("all" by default).
method	specifying which distance method to be used to estimate expression phylogeny in bootstrapping.

Value

returns a data frame of six columns, refer to details for more information.

References

Gu,X. 2016. Understanding tissue expression evolution: from expression phylogeny to phylogenetic network. Brief. Bioinformatics, 17, 249-254.

Examples

data(tetraExp)
gamma.df <- estgamma(tetraExp, taxa = "all",
                     subtaxa = c("Brain", "Cerebellum"),
                     method = "pea")
gamma.df

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