getSelectedTaxonNames: Get a subset of input taxa based on a selected taxonomy rank

In BIONF/PhyloProfile: PhyloProfile

Get a subset of input taxa based on a selected taxonomy rank

Description

Get a subset of taxon ncbi IDs and names from an input list of taxa based on a selected supertaxon (identified by its taxonomy rank and supertaxon name or supertaxon ID).

Usage

getSelectedTaxonNames(inputTaxonIDs = NULL, rank = NULL,
    higherRank = NULL, higherID = NULL, higherName = NULL, taxDB = NULL)

Arguments

inputTaxonIDs	list of input taxon IDs (e.g. c("10116", "122586"))
rank	taxonomy rank of input taxa (e.g. "species")
higherRank	selected taxonomy rank (e.g. "phylum")
higherID	supertaxon ID (e.g. 7711). NOTE: either supertaxon ID or name is required, not neccessary to give both
higherName	supertaxon name (e.g. "Chordata"). NOTE: either supertaxon ID or name is required, not neccessary to give both
taxDB	Path to the taxonomy DB files

Value

A data frame contains ncbi IDs and names of taxa from the input taxon list that belong to the selected supertaxon.

Author(s)

Vinh Tran [e-mail]

Examples

inputTaxonIDs <- c("10116", "122586", "123851", "13616", "188937", "189518",
"208964", "224129", "224324", "237631", "243230")
rank <- "species"
higherRank <- "phylum"
higherID <- 7711
getSelectedTaxonNames(inputTaxonIDs, rank, higherRank, higherID, NULL)
higherName <- "Chordata"
getSelectedTaxonNames(inputTaxonIDs, rank, higherRank, NULL, higherName,NULL)

BIONF/PhyloProfile documentation built on Dec. 18, 2024, 7:33 a.m.