taxdumpHigherRank: Utilities for NCBI Taxdump

In heibl/megaptera: MEGAPhylogeny Techniques in R

Description

Get the taxon name of a certain higher rank for a particular taxon, e.g. get the familiy of Megaptera.

Usage

taxdumpHigherRank(x, taxon, rank, it.max = 30)

Arguments

x	Either an object of class megapteraProj or a data frame containing a taxonomy table in parent-child format as returned by dbReadTaxonomy.
taxon	A vector of mode "character" giving the taxon name.
rank	A vector of mode "character" giving the name of a higher (relative to taxon) rank.
it.max	An integer giving maximum number of iteration in case rank is not present in the lineage of taxon

Value

A character string giving a taxon name.

See Also

ncbiTaxonomy for downloading the NCBI taxonomy and dbReadTaxonomy for reading the project taxonomy; other taxdump-related tools: taxdumpAddNode, taxdumpChildren, taxdumpDropTip, taxdumpMRCA, taxdumpSubset, taxdump2phylo and taxdump_isTerminal.

heibl/megaptera documentation built on Jan. 17, 2021, 3:34 a.m.