do_findPeaks_MSW: Core API function for single-spectrum non-chromatography MS...

In xiaodfeng/DynamicXCMS: LC-MS and GC-MS Data Analysis

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

xiaodfeng/DynamicXCMS documentation built on Aug. 6, 2023, 3:02 p.m.