findChromPeaks-Chromatogram-CentWaveParam: centWave-based peak detection in purely chromatographic data

In sneumann/xcms: LC-MS and GC-MS Data Analysis

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

library(MSnbase)
## Loading a test data set with identified chromatographic peaks
faahko_sub <- loadXcmsData("faahko_sub2")
faahko_sub <- filterRt(faahko_sub, c(2500, 3700))

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

## 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)

library(MsExperiment)
library(xcms)
## Perform peak detection on an MChromatograms object

fls <- 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"))
od3 <- readMsExperiment(fls)

## 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)

sneumann/xcms documentation built on Nov. 3, 2024, 10:33 p.m.