CleanPeaksParam {xcms} | R Documentation |
Remove chromatographic peaks with a retention time range larger than the
provided maximal acceptable width (maxPeakwidth
).
CleanPeaksParam(maxPeakwidth = 10) ## S4 method for signature 'XCMSnExp,CleanPeaksParam' refineChromPeaks(object, param = CleanPeaksParam(), msLevel = 1L)
maxPeakwidth |
for |
object |
XCMSnExp object with identified chromatographic peaks. |
param |
|
msLevel |
|
XCMSnExp
object with chromatographic peaks exceeding the specified
maximal retention time width being removed.
refineChromPeaks
methods will always remove feature definitions, because
a call to this method can change or remove identified chromatographic peaks,
which may be part of features.
Johannes Rainer
Other chromatographic peak refinement methods:
MergeNeighboringPeaksParam
## Perform chromatographic peak detection on a test file. fl <- system.file("microtofq/MM14.mzML", package = "msdata") data <- readMSData(fl, mode = "onDisk") data <- findChromPeaks(data, param = CentWaveParam(peakwidth = c(2, 8))) ## Distribution of chromatographic peak widths quantile(chromPeaks(data)[, "rtmax"] - chromPeaks(data)[, "rtmin"]) ## Remove all chromatographic peaks with a width larger 5 seconds data <- refineChromPeaks(data, param = CleanPeaksParam(5)) quantile(chromPeaks(data)[, "rtmax"] - chromPeaks(data)[, "rtmin"])