MS Data Analysis

Description Usage Arguments Details Value Author(s) See Also

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

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

`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.

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

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.

Joachim Kutzera, Steffen Neumann, Johannes Rainer

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.

anupbharade09/xcms_test documentation built on May 14, 2019, 4:07 a.m.