Modified central log ratio (mclr) transformation extracted from the SPRING package

Usage

mclr(dat, base = exp(1), tol = 1e-16, eps = NULL, atleast = 1)

Arguments

dat: raw count data or compositional data (n by p) does not matter.
base: exp(1) for natural log
tol: tolerance for checking zeros
eps: epsilon in eq (2) of the paper "Yoon, Gaynanova, Müller (2019), Frontiers in Genetics". positive shifts to all non-zero compositions. Refer to the paper for more details. eps = absolute value of minimum of log ratio counts plus c.
atleast: default value is 1. Constant c which ensures all nonzero values to be strictly positive. default is 1.

Value

mclr returns a data matrix of the same dimension with input data matrix.

Details

This function implements the mclr normalization introduced in Yoon G, Gaynanova I and Müller CL (2019) Microbial Networks in SPRING - Semi-parametric Rank-Based Correlation and Partial Correlation Estimation for Quantitative Microbiome Data. Front. Genet. 10:516. doi:10.3389/fgene.2019.00516