retFatMatrix: retFatMatrix

Description

Build a fat data matrix

Usage

retFatMatrix(data)

Arguments

data

the list obtained from gatherInfo()

Value

A fat data matrix containing the area of the deconvoluted and aligned peaks. The row are the samples while the column represent the different peaks.

Details

This function allows to extract the data from an object created using gatherInfo and build a data matrix using the area of the deconvoluted and aligned peaks. The row are the samples while the column represent the different peaks.

Examples

Run this code

require(gcspikelite)
# paths and files
gcmsPath <- paste(find.package("gcspikelite"), "data", sep="/")
cdfFiles <- dir(gcmsPath,"CDF",full=TRUE)
# read data, peak detection results
pd <- peaksDataset(cdfFiles[1:2], mz=seq(50,550),
                   rtrange=c(7.5,8.5))
pd <- addXCMSPeaks(files=cdfFiles[1:2], object=pd,
                   peakPicking=c('mF'), snthresh=3, fwhm=4,
                   step=1, steps=2, mzdiff=0.5)
mp <- correlationAlignment(object=pd, thr=0.85, D=20,
                           penality=0.2, normalize=TRUE,
                           minFilter=1) 
outList <- gatherInfo(pd, mp)
mtxD <- retFatMatrix(data=outList)