physeq_transform_anderson_log: Log-transformation of OTU abundance table.

In vmikk/metagMisc: Miscellaneous functions for metagenomic analysis

Log-transformation of OTU abundance table.

Description

Log-transformation of OTU abundance table.

Usage

physeq_transform_anderson_log(physeq, ...)

Arguments

physeq	A phyloseq-class object
...	Additional arguments (e.g., "logbase" for the logarithm base) will be passed to decostand

Details

Logarithmic transformation as suggested by Anderson et al. (2006) will be applied to the OTU table in phyloseq-object. First, non-integer data will be divided by smallest positive value. Second, log(x) + 1 for x > 0. Default value of the logarithm base ("logbase" parameter) is 2. This function is a wrapper to decostand in vegan.

Value

Phyloseq object with log-transformed counts in OTU table.

References

Anderson MJ, Ellingsen KE and McArdle BH. (2006) Multivariate dispersion as a measure of beta diversity. Ecology Letters 9, P. 683–693.

See Also

decostand

Examples

data(enterotype)
physeq_transform_anderson_log(enterotype)

vmikk/metagMisc documentation built on June 20, 2024, 7:20 a.m.