createRootedTree {PhyloProfile} | R Documentation

## Create rooted tree from a taxonomy matrix

### Description

Create rooted tree from a taxonomy matrix

### Usage

    createRootedTree(df, rootTaxon = NULL)

### Arguments

`df` | data frame contains taxonomy matrix used for generating tree (see distDf in example)
`rootTaxon` | taxon used for rooting the taxonomy tree

### Value

A rooted taxonomy tree as an object of class "phylo".

### Author(s)

Vinh Tran tran@bio.uni-frankfurt.de

### See Also

`taxa2dist` for distance matrix generation from a taxonomy matrix, `getTaxonomyMatrix` for getting taxonomy matrix, `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
    createRootedTree(distDf, "ncbi10090")

[Package PhyloProfile version 1.2.8 Index]