metaX (version 1.4.0)

normalize: Normalisation of peak intensity

Description

The normalize method performs normalisation on peak intensities.

Usage

normalize(para, method = "sum", valueID = "value", ...)

Arguments

para

A metaXpara object.

method

The normalization method: sum, vsn, quantiles, quantiles.robust, sum, pqn. Default is sum.

valueID

The name of the column which will be normalized.

...

Additional parameter

Value

A metaXpara object.

Examples

library(faahKO)
xset <- group(faahko)
xset <- retcor(xset)
xset <- group(xset)
xset <- fillPeaks(xset)
peaksData <- as.data.frame(groupval(xset,"medret",value="into"))
peaksData$name <- row.names(peaksData)
para <- new("metaXpara")
rawPeaks(para) <- peaksData
sampleListFile(para) <- system.file("extdata/faahKO_sampleList.txt", 
    package = "metaX")
para <- reSetPeaksData(para)
para <- metaX::normalize(para)