refineChromPeaks-clean: Remove chromatographic peaks with too large rt width
In yclement/xcms: LC-MS and GC-MS Data Analysis

Description Usage Arguments Value Note Author(s) See Also Examples

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 `CleanPeaksParam`: `numeric(1)` defining the maximal allowed peak width (in retention time).
`object`	XCMSnExp object with identified chromatographic peaks.
`param`	`CleanPeaksParam` object defining the settings for the method.
`msLevel`	`integer` defining for which MS level(s) the chromatographic peaks should be cleaned.

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"])