findChromPeaks,Chromatogram,CentWaveParam-method {xcms} | R Documentation |
findChromPeaks
on a Chromatogram or Chromatograms object with a
CentWaveParam parameter object performs centWave-based peak detection
on purely chromatographic data. See centWave for details on the method
and CentWaveParam for details on the parameter class.
Note that not all settings from the CentWaveParam
will be used.
See peaksWithCentWave()
for the arguments used for peak detection
on purely chromatographic data.
## S4 method for signature 'Chromatogram,CentWaveParam' findChromPeaks(object, param, ...)
object |
a Chromatogram or Chromatograms object. |
param |
a CentWaveParam object specifying the settings for the
peak detection. See |
... |
currently ignored. |
If called on a Chromatogram
object, the method returns a matrix
with
the identified peaks. See peaksWithCentWave()
for details on the matrix
content.
Johannes Rainer
peaksWithCentWave()
for the downstream function and centWave
for details on the method.
od <- readMSData(system.file("cdf/KO/ko15.CDF", package = "faahKO"), mode = "onDisk") ## Extract chromatographic data for a small m/z range chr <- chromatogram(od, mz = c(272.1, 272.3))[1, 1] ## Identify peaks with default settings pks <- findChromPeaks(chr, CentWaveParam()) pks ## Plot the identified peaks plot(chr, type = "h") rect(xleft = pks[, "rtmin"], xright = pks[, "rtmax"], ybottom = rep(0, nrow(pks)), ytop = pks[, "maxo"], col = "#ff000020") ## Modify the settings cwp <- CentWaveParam(snthresh = 5, peakwidth = c(10, 60)) pks <- findChromPeaks(chr, cwp) pks plot(chr, type = "h") rect(xleft = pks[, "rtmin"], xright = pks[, "rtmax"], ybottom = rep(0, nrow(pks)), ytop = pks[, "maxo"], col = "#00ff0020")