lilikoi.preproc_norm: A Normalization function.

In lilikoi: Metabolomics Personalized Pathway Analysis Tool

A Normalization function.

Description

This function is used to preprocess data via normalization. It provides three normalization methods: standard normalization, quantile normalization and median fold normalization. The median fold normalization is adapted from http://www.metabolomics-forum.com/index.php?topic=281.0.

Usage

lilikoi.preproc_norm(
  inputdata = Metadata,
  method = c("standard", "quantile", "median")
)

Arguments

inputdata	An expression data frame with samples in the rows, metabolites in the columns
method	The method to be used to process data, including standard normalization (standard), quantile normalization (quantile) and median fold normalization (median).

Value

A normalized dataset with samples in the rows, metabolites in the columns.

Examples

dt <- lilikoi.Loaddata(file=system.file("extdata",
 "plasma_breast_cancer.csv", package = "lilikoi"))
Metadata <- dt$Metadata
dataSet <- dt$dataSet
lilikoi.preproc_norm(inputdata=Metadata, method="standard")

lilikoi documentation built on Oct. 6, 2022, 1:05 a.m.