retFatMatrix {flagme} | R Documentation |
Build a fat data matrix
retFatMatrix(object, data, minFilter = 1)
object |
peakDataset object |
data |
a gatherInfo() object |
minFilter |
the minimum number for a feature to be returned in the data matrix |
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.
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
Riccardo Romoli riccardo.romoli@unifi.it
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) ma <- multipleAlignment(pd = pd, group = c(1,1), filterMin = 1, metric = 2, type = 2) outList <- gatherInfo(pd, ma) mtxD <- retFatMatrix(object = pd, data = outList, minFilter = 1)