metTransform: Transformation of the dataMatrix

In ethevenot/metabolis: Metabolomics Data Analysis

Description

Transformation of the dataMatrix

Transformation of the dataMatrix

Usage

metTransform(x, ...)

## S4 method for signature 'MultiDataSet'
metTransform(x, methodC = c("log2", "log10",
  "sqrt")[1], info.txtC = NA)

## S4 method for signature 'ExpressionSet'
metTransform(x, methodC = c("log2", "log10",
  "sqrt")[1], info.txtC = NA)

Arguments

x	An S4 object of class MultiDataSet
methodC	Character: Factor of interest (name of a column from the pData(x))
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
x	An S4 object of class ExpressionSet
methodC	Character: Factor of interest (name of a column from the pData(x))
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 the fData data frames

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

Examples

prometMset <- metRead(system.file("extdata/promet", package="metabolis"))
prometMset <- metTransform(prometMset, "sqrt")
printStr <- lapply(assayData(prometMset), function(aData) ropls::strF(aData[["exprs"]]))
sacSet <- metRead(system.file("extdata/sacurine", package = "metabolis"))
ropls::strF(t(exprs(sacSet)))
sacSet <- metTransform(sacSet, "log2")
ropls::strF(t(exprs(sacSet)))

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