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

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

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

 NULL
#> NULL