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

## matchedFilter-based peak detection in purely chromatographic data

### Description

`findChromPeaks` on a Chromatogram or MChromatograms 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 MChromatograms 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

    ## Loading a test data set with identified chromatographic peaks
    data(faahko_sub)
    ## Update the path to the files for the local system
    dirname(faahko_sub) <- system.file("cdf/KO", package = "faahKO")
    faahko_sub <- filterRt(faahko_sub, c(2500, 3700))

    ##
    od <- as(filterFile(faahko_sub, 1L), "OnDiskMSnExp")

    ## 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)

[Package xcms version 3.16.1 Index]