amp_rename: Used for cleaning and renaming taxonomy in phyloseq objects

In MadsAlbertsen/ampvis: Tools for visualising amplicon data

Description

Used internally in other ampvis functions.

Usage

amp_rename(data)

Arguments

data	(required) A ampvis formated list with all data.
tax.class	Converts a specific phyla to class level instead (e.g. "p__Proteobacteria").
tax.empty	Either "remove" OTUs without taxonomic information at X level, with "best" classification or add the "OTU" name (default: best).
tax.level	The taxonomic level to remove OTUs with empty taxonomy, only used when tax.empty = "remove" (default: Genus).

Value

A phyloseq object with cleaned and renamed taxonomy.

Author(s)

Mads Albertsen [e-mail]

MadsAlbertsen/ampvis documentation built on May 7, 2019, 2:08 p.m.