taxFromWorms: Retrieves Taxonomy from World Register of Marine Species

In pmartinezarbizu/dada2pp: Miscelaneous Functions for Post-Processing dada2 Results.

Retrieves Taxonomy from World Register of Marine Species

Description

Query a vector to taxa names against WORMS and retrives valid names and classification

Usage

taxFromWorms(x, ...)

Arguments

x	A vector of species names
...	additional arguments passed to worms::wormsmatchsp and worms::wormsmatchgen.

Details

The taxonomic assignment of the ASVs resulting from blasting against GenBank is not allways up to date. This fuction will query the names against Worl Register of Marine Species at https://www.marinespecies.org/ by using the package worms. The function returns a data.frame with the columns "kingdom", "phylum", "class", "order", "family", "genus", "AphiaID", "status", "scientificname", "valid_name" and"query_name".

The function assumes that the separator between genus name and species name is either a space or an underscore.

Author(s)

Pedro Martinez Arbizu

See Also

worms

Examples

data(deepMeio)
tax_deepMeio <- taxFromWorms(deepMeio$Species[1:51])

#example retrieve non only marine species 
tax_deepMeio <- taxFromWorms(deepMeio$Species[1:51], marine_only=FALSE)

pmartinezarbizu/dada2pp documentation built on Feb. 7, 2024, 7:01 a.m.