normalize: Normalisation of peak intensity

In wenbostar/metaX: A flexible and comprehensive software for processing omics data.

Normalisation of peak intensity

Description

The normalize method performs normalisation on peak intensities.

Usage

normalize(para, method = "sum", valueID = "value", norFactor = NULL,
  useClass = FALSE, ...)

Arguments

para	A metaXpara object.
method	The normalization method: sum, median, vsn, quantiles, quantiles.robust, sum, pqn, combat and tmm. Default is sum.
valueID	The name of the column which will be normalized.
norFactor	The factor that will be used for normalization. This is usually used in urine data normalization. The factor is the column name in sample list file that contains the normalization factor value, such as the value "osmolality". Default the value is NULL. Only if the value of norFactor is not NULL and the parameter "method" is NULL, this normalization will work.
useClass	Whether or not to use class information when perform batch correction using ComBat method. Default is False.
...	Additional parameter

Value

A metaXpara object.

Author(s)

Bo Wen [e-mail]

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)

wenbostar/metaX documentation built on July 4, 2023, 7:50 p.m.