do_findPeaks_MSW {xcms} | R Documentation

## Core API function for single-spectrum non-chromatography MS data peak detection

### Description

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

### Usage

    do_findPeaks_MSW(mz, int, snthresh = 3, verboseColumns = FALSE, ...)

### Arguments

`mz` | Numeric vector with the individual m/z values from all scans/ spectra of one file/sample.
`int` | Numeric vector with the individual intensity values from all scans/spectra of one file/sample.
`snthresh` | `numeric(1)` defining the signal to noise ratio cutoff.
`verboseColumns` | `logical(1)` whether additional peak meta data columns should be returned.
`...` | Additional parameters to be passed to the `peakDetectionCWT` function.

### Details

This is a wrapper around the peak picker in Bioconductor's `MassSpecWavelet` package calling `peakDetectionCWT` and `tuneInPeakInfo` functions. See the xcmsDirect vignette for more information.

### Value

A matrix, each row representing an identified 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 standard user interface method. `peakDetectionCWT` from the `MassSpecWavelet` package.

Other core peak detection functions: `do_findChromPeaks_centWaveWithPredIsoROIs`, `do_findChromPeaks_centWave`, `do_findChromPeaks_massifquant`, `do_findChromPeaks_matchedFilter`

[Package xcms version 3.2.0 Index]