IntCorrection: Intensity correction using serial QC samples

In Waddlessss/MAFFIN: Integrated Sample Normalization by MAFFIN Algorithm

Intensity correction using serial QC samples

Description

Correct MS signal intensities using serial QC samples

Usage

IntCorrection(
  FeatureTable,
  IntThreshold = 0,
  LR_QC_points = 5,
  QR_QC_points = 7,
  SQCcor = 0.9,
  SampleInCol = TRUE,
  output = FALSE
)

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.
LR_QC_points	Minimum serial QC data points for quadratic regression.
QR_QC_points	Minimum serial QC data points for cubic regression.
SQCcor	Pearson's correlation threshold for serial QC samples (recommend: 0.8-0.9).
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. For group names, please use:
"QC" for quality control samples between real samples (normal QC samples);
"SQC_###" for serial QC samples with a certain loading amount. For example, SQC_1.0 means a serial QC sample with injection volume of 1.0 uL.
Please note, group names of real biological samples cannot be "RT" and "blank".
An example of FeatureTable is provided as TestingData in this package.

Value

This function will return the original feature table with corrected intensities.

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

intCorrectedTable = IntCorrection(TestingData)

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