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

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.