findPeaks.MSW,xcmsRaw-method {xcms} | R Documentation

## Peak detection for single-spectrum non-chromatography MS data

### Description

This method performs peak detection in mass spectrometry direct injection spectrum using a wavelet based algorithm.

### Usage

    ## S4 method for signature 'xcmsRaw'
    findPeaks.MSW(object, snthresh = 3, verbose.columns = FALSE, ...)

### Arguments

`object` | The `xcmsRaw` object on which peak detection should be performed.
`snthresh` | `numeric(1)` defining the signal to noise ratio cutoff.
`verbose.columns` | Logical whether additional peak meta data columns should be returned.
`...` | Additional parameters to be passed to the `identifyMajorPeaks` and `sav.gol` functions from the `MassSpecWavelet` package.

### Details

This is a wrapper around the peak picker in Bioconductor's `MassSpecWavelet` package calling `peakDetectionCWT` and `tuneInPeakInfo` functions.

### Value

A matrix, each row representing an intentified peak, with columns:

mz

  m/z value of the peak at the centroid position.

mzmin

  Minimum m/z of the peak.

mzmax

  Maximum m/z of the peak.

rt

  Always `-1`.

rtmin

  Always `-1`.

rtmax

  Always `-1`.

into

  Integrated (original) intensity of the peak.

maxo

  Maximum intensity of the peak.

intf

  Always `NA`.

maxf

  Maximum MSW-filter response of the peak.

sn

  Signal to noise ratio.

### Author(s)

Joachim Kutzera, Steffen Neumann, Johannes Rainer

### See Also

`MSW` for the new user interface, `do_findPeaks_MSW` for the downstream analysis function or `peakDetectionCWT` from the `MassSpecWavelet` for details on the algorithm and additionally supported parameters.

[Package xcms version 3.10.2 Index]