addXCMSPeaks {flagme} | R Documentation |
Reads the raw data using xcms, group each extracted ion
according to their retention time using CAMERA and attaches them to an
already created peaksDataset
object
addXCMSPeaks(files, object, peakPicking=c('cwt','mF'), ...)
files |
character vector of same length as |
object |
a |
peakPicking |
Methods to use for peak detection. See details. |
... |
arguments passed on to |
Repeated calls to xcmsSet and annotate to perform peak-picking and
deconvolution. The peak detection results are added to the original
peaksDataset
object. Two peak detection alorithms are
available: continuous wavelet transform (peakPicking=c('cwt')) and the
matched filter approach (peakPicking=c('mF')) described by Smith et al
(2006). For further information consult the xcms package manual.
peaksDataset
object
Riccardo Romoli riccardo.romoli@unifi.it
peaksDataset
findPeaks.matchedFilter
findPeaks.centWave
xcmsRaw-class
# need access to CDF (raw data) require(gcspikelite) gcmsPath <- paste(find.package("gcspikelite"), "data", sep="/") # full paths to file names cdfFiles <- dir(gcmsPath, "CDF", full=TRUE) # create a 'peaksDataset' object and add XCMS peaks to it pd <- peaksDataset(cdfFiles[1], mz=seq(50,550), rtrange=c(7.5,8.5)) pd <- addXCMSPeaks(cdfFiles[1], pd, peakPicking=c('mF'), snthresh=3, fwhm=4, step=1, steps=2, mzdiff=0.5)