shiftCor: shiftCor

In idrblab/NOREVA: R Package for Systematic Optimization of Metabolomic Data Processing

shiftCor

Description

shiftCor provides the QC-RLS correction for large scale metabolomics. See the details at the following References.

Usage

shiftCor(
  samPeno,
  samFile,
  Frule = 0.8,
  QCspan = 0.75,
  degree = 2,
  imputeM = "KNN"
)

Arguments

samPeno	a file with the meta information.
samFile	a file with the expression information.
Frule	The cut-off value for missing value filter function.
QCspan	The smoothing parameter which controls the bias-variance tradeoff. if the QCspan is set at '0', the generalised cross-validation will be performed to avoid overfitting the observed data.
degree	Lets you specify local constant regression (i.e., the Nadaraya-Watson estimator, degree=0), local linear regression (degree=1), or local polynomial fits (degree=2, the default).
imputeM	The parameter for imputation method.(i.e., nearest neighbor averaging, "KNN"; minimum values for imputed variables, "min", median values for imputed variables (Group dependent) "median").

References

statTarget: a streamlined tool for signal drift correction and interpretations of quantitative mass spectrometry-based omics data. Luan H, Ji F, Chen Y, Cai Z. 2018, Analytica Chimica Acta.

Examples

library(statTarget)
datpath <- system.file("extdata",package = "statTarget")
samPeno <- paste(datpath,"MTBLS79_sampleList.csv", sep="/")
samFile <- paste(datpath,"MTBLS79.csv", sep="/")
shiftCor(samPeno,samFile,Frule = 0.8,QCspan = 0.75, degree = 2,imputeM = "KNN")

idrblab/NOREVA documentation built on April 17, 2025, 2:04 p.m.