clr: Centered log-ratio (CLR) transform

In hallucigenia-sparsa/seqgroup: Analysis of Sequencing Data with Groups

Centered log-ratio (CLR) transform

Description

In the CLR transform, each entry is divided by the geometric mean of its sample and then the logarithm is taken.

Usage

clr(
  abundances,
  minocc = 0,
  pseudocount = 1,
  scale.factor = 1,
  omit.zeros = FALSE
)

Arguments

abundances	a matrix with taxa as rows and samples as columns
minocc	prevalence filter; ignored if 0 or below
pseudocount	zero replacement value; should be above 0
scale.factor	scaling factor; abundances will be multiplied with this factor
omit.zeros	if TRUE, ignore pseudocount and compute clr transform only on non-zero elements

Details

When omit.zeros is set to true, the default behaviour of clr in the compositions package when applied column-wise is reproduced.

Value

clr-transformed matrix

hallucigenia-sparsa/seqgroup documentation built on July 6, 2022, 1:11 p.m.