metCorrect: Signal drift and batch effect correction

In ethevenot/metabolis: Metabolomics Data Analysis

Description

Signal drift and batch effect correction

Signal drift and batch effect correction

Usage

metCorrect(x, ...)

## S4 method for signature 'MultiDataSet'
metCorrect(x, referenceSampleTypeC = c("pool",
  "sample")[1], colnameBatchC = "batch",
  colnameInjectionOrderC = "injectionOrder",
  colnameSampleTypeC = "sampleType", spanN = 1, fig.pdfC = NA,
  info.txtC = NA)

## S4 method for signature 'ExpressionSet'
metCorrect(x, referenceSampleTypeC = c("pool",
  "sample")[1], colnameBatchC = "batch",
  colnameInjectionOrderC = "injectionOrder",
  colnameSampleTypeC = "sampleType", spanN = 1, fig.pdfC = NA,
  info.txtC = NA)

Arguments

x	An S4 object of class MultiDataSet
colnameBatchC	Character: name of the column from pData(x) containing the batch information (encoded as characters)
colnameSampleTypeC	Character: name of the column from pData(x) containing the sample type information (encoded as characters)
spanN	Numeric: smoothing parameter for the loess regression; between 0 and 1; (default set to 1)
fig.pdfC	Character: Name of the file for the graphics from the significant features; if NA, the graphics are displayed on the screen;
info.txtC	Character: File name for the printed results (call to 'sink()'); if NA (default), messages will be printed on the screen; if NULL, no verbose will be generated
referenceSampeTypeC	Character: sample type to be used as reference for the correction (as indicated in the 'colnameSampleType' column from the pData(x); e.g. 'pool')
colnameInjectionOrder	Character: name of the column from pData(x) containing the injection order information (encoded as numerics)
x	An S4 object of class ExpressionSet
referenceSampeTypeC	Character: sample type to be used as reference for the correction (as indicated in the 'colnameSampleType' column from the pData(x); e.g. 'pool')
colnameBatchC	Character: name of the column from pData(x) containing the batch information (encoded as characters)
colnameInjectionOrder	Character: name of the column from pData(x) containing the injection order information (encoded as numerics)
colnameSampleTypeC	Character: name of the column from pData(x) containing the sample type information (encoded as characters)
spanN	Numeric: smoothing parameter for the loess regression; between 0 and 1; (default set to 1)
fig.pdfC	Character: Name of the file for the graphics from the significant features; if NA, the graphics are displayed on the screen;
info.txtC	Character: File name for the printed results (call to 'sink()'); if NA (default), messages will be printed on the screen; if NULL, no verbose will be generated

Value

MultiDataSet including the adjusted p-values in fData (or the vector of adjusted p-values when returnAdjustOnlyL is TRUE)

ExpressionSet including the adjusted p-values in fData (or the vector of adjusted p-values when returnAdjustOnlyL is TRUE)

Examples

# to be provided
sacSet <- metRead(system.file("extdata/sacurine", package = "metabolis"))
sacSet <- metCorrect(sacSet)

ethevenot/metabolis documentation built on June 28, 2019, 1:27 p.m.