abundances: Abundance Matrix from Phyloseq

In microbiome/microbiome: Microbiome Analytics

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', 'alr', or any method from the vegan::decostand function.

Value

Abundance matrix (OTU x samples).

Author(s)

Contact: Leo Lahti [e-mail]

References

See citation('microbiome')

Examples

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

microbiome/microbiome documentation built on Aug. 22, 2023, 7:12 a.m.