rename_OTU: Rename each taxon

rename_OTUR Documentation

Rename each taxon

Description

rename_OTU assigns a non - repeated name to each bacteria for a given taxonomic level.

Usage

rename_OTU(phy, rank, db = "SILVA")

Arguments

phy

the phyloseq object where the information is contained.

rank

a numeric value indicating the taxonomic level where the names should be taken. It corresponds with the column number of phy@tax_table associated to the desired taxonomic rank.

db

the bacterial database used to name each OTU of the phyloseq object: SILVA (default) or GreenGenes.

Value

A vector with the names for each bacteria. It has not repeated names and none of them starts with Incertae_Sedis or unclassified.


malucalle/selbal documentation built on May 31, 2024, 2:36 p.m.