findChromPeaks,Chromatogram,MatchedFilterParam-method {xcms} | R Documentation

## matchedFilter-based peak detection in purely chromatographic data

### Description

`findChromPeaks` on a Chromatogram or Chromatograms object with a MatchedFilterParam parameter object performs matchedFilter-based peak detection on purely chromatographic data. See matchedFilter for details on the method and MatchedFilterParam for details on the parameter class. Note that not all settings from the `MatchedFilterParam` will be used. See `peaksWithMatchedFilter()` for the arguments used for peak detection on purely chromatographic data.

### Usage

    ## S4 method for signature 'Chromatogram,MatchedFilterParam'
    findChromPeaks(object, param, ...)

### Arguments

`object` | a Chromatogram or Chromatograms object.
`param` | a MatchedFilterParam object specifying the settings for the peak detection. See `peaksWithMatchedFilter()` for the description of arguments used for peak detection.
`...` | currently ignored.

### Value

If called on a `Chromatogram` object, the method returns a `matrix` with the identified peaks. See `peaksWithMatchedFilter()` for details on the matrix content.

### Author(s)

Johannes Rainer

### See Also

`peaksWithMatchedFilter()` for the downstream function and matchedFilter for details on the method.

### Examples

    od <- readMSData(system.file("cdf/KO/ko15.CDF", package = "faahKO"),
        mode = "onDisk")

    ## Disabling parallel processing in this example
    register(SerialParam())

    ## 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, MatchedFilterParam())

    ## Plot the identified peaks
    plot(xchr)

    ## Modify the settings
    mfp <- MatchedFilterParam(fwhm = 60)
    xchr <- findChromPeaks(chr, mfp)

    plot(xchr)

[Package xcms version 3.10.2 Index]