make_clr: Normalization Functions

View source: R/normalizers.R

make_clrR Documentation

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 April 24, 2024, 5 p.m.