make_clr: Normalization Functions

In jbisanz/qiime2R: qiime2R

Normalization Functions

Description

Takes a numeric table and transforms to a number of options as below. Note: Rows are expected to be features and columns are expected to be sample IDs. * 'make_clr()' A centered log2-ratio (columns sum to ~0). See and cite 10.1139/cjm-2015-0821 * 'make_percent()' Convert to percent (columns sum to 100) * 'make_proportion()' Convert to proportion (columns sum to 1)

Usage

make_clr(features, prior, czm)

Arguments

features	Table of feature/OTU/SV counts where Samples are columns, and IDs are row names. Expects matrix or data.frame.
prior	Only relevant to CLR: A numeric value to add before log transformation (default 0.5). *Ignored if CZM=TRUE
czm	Only relevant to CLR: Should count zero multiplicative method be used instead of adding simple prior (TRUE/FALSE, defaults to FALSE)

Value

Table of normalized abundances

jbisanz/qiime2R documentation built on March 19, 2024, 12:41 p.m.