getSelectedTaxonNames {PhyloProfile}R Documentation

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, 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 tran@bio.uni-frankfurt.de

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)

[Package PhyloProfile version 1.8.0 Index]