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

## centWave-based peak detection in purely chromatographic data

### Description

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

After chromatographic peak detection, identified peaks can also be refined with the `refineChromPeaks()` method, which can help to reduce peak detection artifacts.

### Usage

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

    ## S4 method for signature 'MChromatograms,CentWaveParam'
    findChromPeaks(object, param, BPPARAM = bpparam(), ...)

    ## S4 method for signature 'MChromatograms,MatchedFilterParam'
    findChromPeaks(object, param, BPPARAM = BPPARAM, ...)

### Arguments

`object` | a Chromatogram or MChromatograms object.
`param` | a CentWaveParam object specifying the settings for the peak detection. See `peaksWithCentWave()` for the description of arguments used for peak detection.
`...` | currently ignored.
`BPPARAM` | a parameter class specifying if and how parallel processing should be performed (only for `XChromatograms` objects). It defaults to `bpparam()`. See `bpparam()` for more information.

### Value

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

### Author(s)

Johannes Rainer

### See Also

`peaksWithCentWave()` for the downstream function and centWave 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, CentWaveParam())
    xchr

    ## Plot data and identified peaks.
    plot(xchr)

    ## Perform peak detection on an MChromatograms object
    od3 <- readMSData(c(system.file("cdf/KO/ko15.CDF", package = "faahKO"),
        system.file("cdf/KO/ko16.CDF", package = "faahKO"),
        system.file("cdf/KO/ko18.CDF", package = "faahKO")),
        mode = "onDisk")

    ## Disable parallel processing for this example
    register(SerialParam())

    ## Extract chromatograms for a m/z - retention time slice
    chrs <- chromatogram(od3, mz = 344, rt = c(2500, 3500))

    ## Perform peak detection using CentWave
    xchrs <- findChromPeaks(chrs, param = CentWaveParam())
    xchrs

    ## Extract the identified chromatographic peaks
    chromPeaks(xchrs)

    ## plot the result
    plot(xchrs)

[Package xcms version 3.16.1 Index]