EvaPRMAD: Calculate pooled RMAD for normalization evaluation.

In Waddlessss/MAFFIN: Integrated Sample Normalization by MAFFIN Algorithm

Calculate pooled RMAD for normalization evaluation.

Description

Calculate pooled relative median absolute deviation for each metabolic feature.

Usage

EvaPRMAD(FeatureTable, GroupNames, SampleInCol = TRUE, output = FALSE)

Arguments

FeatureTable	Data frame with features in row and samples in column (default).
GroupNames	A character vector indicating the names of each group.
SampleInCol	TRUE if samples are in column. FALSE if samples are in row.
output	TRUE will output the result table in current working directory

Details

FeatureTable contains measured 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. An example of FeatureTable is provided as TestingData in this package.

Value

This function will return a vector that contains the calculated PRMADs for all features.

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).

Examples

prmad = EvaPRMAD(TestingData, GroupNames=c("HY", "SX", "SW", "YC"))

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