QuantileNorm: Quantile normalization.

In Waddlessss/MAFFIN: Integrated Sample Normalization by MAFFIN Algorithm

Quantile normalization.

Description

Quantile sample normalization.

Usage

QuantileNorm(
  FeatureTable,
  IntThreshold = 0,
  SampleInCol = TRUE,
  output = FALSE,
  OutputNormFactors = FALSE,
  RunEvaluation = TRUE
)

Arguments

FeatureTable	Data frame with features in row and samples in column (default).
IntThreshold	A numeric value indicating the feature intensity threshold. Feature is detected when its intensity larger than this value.
SampleInCol	TRUE if samples are in column. FALSE if samples are in row.
output	TRUE will output the result table in current working directory
OutputNormFactors	TRUE will print the normalization factors after normalization
RunEvaluation	TRUE will evaluate the normalization results using intragroup variation.

Details

FeatureTable contains measured or corrected signal intensities of metabolic features, with features in row and samples in column (default). The column names should be sample names, and the first row should be sample group names (e.g. control, case).
The first column should be unique feature identifiers. For group names, please do not use "blank", "RT", "QC", or "SQC_###" for real biological samples.
An example of FeatureTable is provided as TestingData in this package.

Value

This function will return a list that contains four items if RunEvaluation = TRUE: the normalized feature table, normalization factors, PRMAD of original data, and PRMAD of normalized data. The last two items will not be generated if RunEvaluation = FASLE

References

Yu, Huaxu, and Tao Huan. "MAFFIN: Metabolomics Sample Normalization Using Maximal Density Fold Change with High-Quality Metabolic Features and Corrected Signal Intensities." bioRxiv (2021).
Bolstad, Benjamin M., et al. "A comparison of normalization methods for high density oligonucleotide array data based on variance and bias." Bioinformatics 19.2 (2003): 185-193.

Examples

QuantileNormedTable = QuantileNorm(TestingData)

Waddlessss/MAFFIN documentation built on Aug. 5, 2023, 8:10 p.m.