Peak detection for single-spectrum non-chromatography MS data

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

Usage

# S4 method for class '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 peakDetectionCWT and identifyMajorPeaks functions from the MassSpecWavelet package.

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.

Details

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

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.

Author

Joachim Kutzera, Steffen Neumann, Johannes Rainer