sortTaxaFromTree {PhyloProfile} | R Documentation

## Get sorted supertaxon list based on a rooted taxonomy tree

### 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 tran@bio.uni-frankfurt.de

### 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)

[Package PhyloProfile version 1.0.7 Index]