commonTax.to.NCBI.TaxID: Convert a taxon name to an NCBI taxon ID

In biodiversity-aq/OmicsMetaData: OmicsMetaData: an R-package for interoperable and re-usable biodiversity 'omics (meta)data

Description

converts taxon names of common taxa (superkingdom and phylum level) to it's NCBI taxID using an internal library. For taxa not in the internal library, please see https://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi

Usage

commonTax.to.NCBI.TaxID(taxon, fill.unknown = "12908")

Arguments

taxon	character or character vector. The taxon names to be converted to NCBI tax IDs.
fill.unknown	character. The string to return when a taxon was not found in the list with common taxa. Default is NCBI:txid12908 (the ID for "unknown sequences"), other options include NA or ""

Details

This function makes use of a limited internal library, not all the taxIDs are present

Value

a character or character vector with the matching taxon IDs, with fill.unknown for those not found.

Author(s)

Maxime Sweetlove

Examples

OmicsMetaData:::commonTax.to.NCBI.TaxID("soil metagenome", fill.unknown="12908")

biodiversity-aq/OmicsMetaData documentation built on Dec. 19, 2021, 9:44 a.m.