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

In BIONF/PhyloProfile: PhyloProfile

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 [e-mail]

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 Nov. 2, 2024, 11:44 p.m.