gamma: Estimating gamma from taxaExp objects.

Description Usage Arguments Value References Examples

Description

Estimating gamma from taxaExp objects.

Usage

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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

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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.