Description Usage Arguments Value Author(s) References Examples
Retrieves the taxon abundance table from phyloseq-class object and ensures it is systematically returned as taxa x samples matrix.
1 | abundances(x, transform = "identity")
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x |
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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. |
Abundance matrix (OTU x samples).
Contact: Leo Lahti microbiome-admin@googlegroups.com
See citation('microbiome')
1 2 3 | data(dietswap)
a <- abundances(dietswap)
# b <- abundances(dietswap, transform='compositional')
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