PerformNormalization: Function to perform normalization

In xia-lab/MicrobiomeAnalystR: MicrobiomeAnalystR - A comprehensive R package for statistical, visual, and functional analysis of the microbiome.

Function to perform normalization

Description

This function performs normalization on the uploaded data.

Usage

PerformNormalization(
  mbSetObj,
  rare.opt,
  scale.opt,
  transform.opt,
  isAutoScale = F
)

Arguments

mbSetObj	Input the name of the mbSetObj.
rare.opt	Character, "rarewi" to rarefy the data and "none" to not.
scale.opt	Character, input the name of the data scaling option. "colsum" for total sum scaling, "CSS" for cumulative sum scaling, "upperquartile" for upper-quartile normalization, and "none" to none.
transform.opt	Character, input the name of the data transformation to be applied. "rle" for relative log expression, "TMM" for trimmed mean of M-values, "clr" for centered log ratio, and "none" for none.

Author(s)

Jeff Xia [e-mail] McGill University, Canada License: GNU GPL (>= 2)

xia-lab/MicrobiomeAnalystR documentation built on Feb. 24, 2025, 5:36 a.m.