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, ...) ## S4 method for signature 'Chromatograms,CentWaveParam' findChromPeaks(object, param, BPPARAM = bpparam(), ...) ## S4 method for signature 'Chromatograms,MatchedFilterParam' findChromPeaks(object, param, BPPARAM = BPPARAM, ...)
object |
a Chromatogram or Chromatograms object. |
param |
a CentWaveParam object specifying the settings for the
peak detection. See |
... |
currently ignored. |
BPPARAM |
a parameter class specifying if and how parallel processing
should be performed (only for |
If called on a Chromatogram
object, the method returns an XChromatogram
object with the identified peaks. See peaksWithCentWave()
for details on
the peak 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 xchr <- findChromPeaks(chr, CentWaveParam()) xchr ## Plot data and identified peaks. plot(xchr) ## Modify the settings cwp <- CentWaveParam(snthresh = 5, peakwidth = c(10, 60)) xchr <- findChromPeaks(chr, cwp) xchr plot(xchr) ## Perform peak detection on an Chromatograms object od3 <- readMSData(c(system.file("cdf/KO/ko15.CDF", package = "faahKO"), system.file("cdf/KO/ko16.CDF", package = "faahKO"), system.file("cdf/KO/ko18.CDF", package = "faahKO")), mode = "onDisk") ## Extract chromatograms for a m/z - retention time slice chrs <- chromatogram(od3, mz = 344, rt = c(2500, 3500)) ## Perform peak detection using CentWave xchrs <- findChromPeaks(chrs, param = CentWaveParam()) xchrs ## Extract the identified chromatographic peaks chromPeaks(xchrs) ## plot the result plot(xchrs)