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

In PhyloProfile: PhyloProfile

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, rank, higherRank, higherID,
    higherName)

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.

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)

PhyloProfile documentation built on March 27, 2021, 6:01 p.m.