taxa_quants: Compares taxa quantification from a measurement to a...

In Gibbons-Lab/mbtools: Provides helper functions for microbiome preprocessing and analysis

Compares taxa quantification from a measurement to a reference ground truth.

Description

Note that both arguments must be phyloseq objects from the phyloseq package.

Usage

taxa_quants(ps, ref, normalize = FALSE)

Arguments

ps	A phyloseq object describing the measurements
ref	A phyloseq object describing the reference set. Can be obtained from mockrobiota.
normalize	Whether to normalize taxa counts first.

Value

A data frame with the following columns:

level

The taxonomy level for the entry.

name

The taxonomy.

sample

The sample name for the quantification.

measured

The measured quantification.

reference

The reference quantification.

Examples

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Gibbons-Lab/mbtools documentation built on Jan. 28, 2024, 11:08 a.m.