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:
FilterIntensityParam
,
MergeNeighboringPeaksParam
## Load a test data set with detected peaks data(faahko_sub) ## Update the path to the files for the local system dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO") ## Disable parallel processing for this example register(SerialParam()) ## Distribution of chromatographic peak widths quantile(chromPeaks(faahko_sub)[, "rtmax"] - chromPeaks(faahko_sub)[, "rtmin"]) ## Remove all chromatographic peaks with a width larger 60 seconds data <- refineChromPeaks(faahko_sub, param = CleanPeaksParam(60)) quantile(chromPeaks(data)[, "rtmax"] - chromPeaks(data)[, "rtmin"])