Common Transformations

Common Transformations

getProportions(x)

getCLR(x)

Arguments

x

phyloseq object

Value

Transformed phyloseq

Details

Common transformation in microbiome like proportions, clr.

getProportions convert counts to relative abundance.

getCLR convert counts to centred log transform 'clr'

References

Shetty SA (2020). Utilities for microbiome analytics. https://github.com/RIVM-IIV-Microbiome/biomeUtils

Author

Sudarshan A. Shetty

Examples

library(biomeUtils)
data("FuentesIliGutData")
ps.rel <- getProportions(FuentesIliGutData)
ps.clr <- getCLR(FuentesIliGutData)