perturb: Compositionally perturb a relative-abundance matrix

In mikemc/metacal: Bias estimation and calibration for metagenomics experiments

Description

The perturbation of two compositional vectors v and y is given (up to compositional equivalence) by the elementwise product v * y.

Usage

perturb(x, y, ...)

## S3 method for class 'matrix'
perturb(x, y, margin, norm = "close")

## S3 method for class 'otu_table'
perturb(x, y, norm = "close")

## S3 method for class 'phyloseq'
perturb(x, y, norm = "close")

## S3 method for class 'mc_bias_fit'
perturb(x, y)

Arguments

x	An abundance matrix or phyloseq object containing one
y	A numeric vector with which to perturb the observations in x
margin	Matrix margin that corresponds to observations (samples); 1 for rows, 2 for columns
norm	String specifying how to normalize the perturbed observations; see Details.

Details

Let w = v * y, where v is a row or column of x. The normalization options specified by the norm argument are

• "close" Return the compositional closure of w into the simplex, w / sum(w)

• "keep" Keep the same total abundance as the original vector by returning w * sum(v) / sum(w)

• "none" Return w without any normalization

If y is named, then the names must agree with the taxa names in x and will be used to reorder y to match the taxa order in x.

See Also

calibrate()

mikemc/metacal documentation built on Feb. 20, 2022, 1:46 a.m.