mclr: Modified central log ratio (mclr) transformation

In GraceYoon/SPRING: Semi-Parametric Rank-based approach for INference in Graphical model (SPRING)

Modified central log ratio (mclr) transformation

Description

Modified central log ratio (mclr) transformation

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, M\"uller (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.

Examples

data(QMP)
RMP <- QMP/rowSums(QMP)
mclr_RMP <- mclr(RMP)

GraceYoon/SPRING documentation built on June 29, 2022, 4:14 p.m.