sortTaxaFromTree: Get sorted supertaxon list based on a rooted taxonomy tree

In PhyloProfile: PhyloProfile

Description

Get sorted supertaxon list based on a rooted taxonomy tree

Usage

sortTaxaFromTree(tree)

Arguments

tree	an "phylo" object for a rooted taxonomy tree

Value

A list of sorted taxa obtained the input taxonomy tree.

Author(s)

Vinh Tran [e-mail]

See Also

ppTaxonomyMatrix for a demo taxonomy matrix data

Examples

data("ppTaxonomyMatrix", package = "PhyloProfile")
# prepare matrix for calculating distances
distDf <- subset(ppTaxonomyMatrix, select = -c(ncbiID, fullName))
row.names(distDf) <- distDf$abbrName
distDf <- distDf[, -1]
# create taxonomy tree rooted by ncbi10090
rootedTree <- createRootedTree(distDf, "ncbi10090")
# get taxon list sorted from tree
sortTaxaFromTree(rootedTree)

PhyloProfile documentation built on March 27, 2021, 6:01 p.m.