sortInputTaxa: Sort list of (super)taxa based on a selected reference...

View source: R/parsePhyloProfile.R

sortInputTaxaR 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, sortedTaxonList = NULL, taxDB = 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

sortedTaxonList

list of sorted taxa (optional). Default = NULL

taxDB

Path to the taxonomy DB files

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, createUnrootedTree, sortTaxaFromTree, getInputTaxaName, getInputTaxaID, createLongMatrix

Examples

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

BIONF/PhyloProfile documentation built on Feb. 18, 2024, 7:42 a.m.