sortInputTaxa {PhyloProfile} | R Documentation

## Sort list of (super)taxa based on a selected reference (super)taxon

### Description

Sort list of (super)taxa based on a selected reference (super)taxon

### Usage

    sortInputTaxa(taxonIDs = NULL, rankName, refTaxon = NULL,
        taxaTree = NULL)

### Arguments

`taxonIDs` | list of taxon IDs (e.g.: ncbi1234, ncbi9999, ...). Default = NULL.
`rankName` | working taxonomy rank (e.g. "species", "phylum",...)
`refTaxon` | selected reference taxon. Default = NULL.
`taxaTree` | taxonomy tree for the input taxa (optional). Default = NULL.

### Value

A taxonomy matrix for the input taxa ordered by the selected reference taxon. This matrix is sorted either based on the NCBI taxonomy info, or based on an user-defined taxonomy tree (if provided).

### Author(s)

Vinh Tran tran@bio.uni-frankfurt.de

### See Also

`getNameList`, `getTaxonomyMatrix`, `createRootedTree`, `sortTaxaFromTree`, `getInputTaxaName`, `getInputTaxaID`, `createLongMatrix`

### Examples

    taxonIDs <- c(
        "ncbi10116", "ncbi123851", "ncbi3702", "ncbi13616", "ncbi9606"
    )
    sortInputTaxa(taxonIDs, "species", "Homo sapiens", NULL)

[Package PhyloProfile version 1.2.8 Index]