abundances {microbiome} | R Documentation

## Abundance Matrix from Phyloseq

### Description

Retrieves the taxon abundance table from phyloseq-class object and ensures it is systematically returned as taxa x samples matrix.

### Usage

    abundances(x, transform = "identity")

### Arguments

`x` | `phyloseq-class` object
`transform` | Transformation to apply. The options include: 'compositional' (ie relative abundance), 'Z', 'log10', 'log10p', 'hellinger', 'identity', 'clr', or any method from the vegan::decostand function.

### Value

Abundance matrix (OTU x samples).

### Author(s)

Contact: Leo Lahti microbiome-admin@googlegroups.com

### References

See citation('microbiome')

### Examples

    data(dietswap)
    a <- abundances(dietswap)
    # b <- abundances(dietswap, transform='compositional')

[Package microbiome version 1.12.0 Index]