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

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,
  scantime = numeric(),
  valsPerSpect = integer(),
  ...
)

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.

scantime

ignored.

valsPerSpect

ignored.

...

Additional parameters to be passed to the peakDetectionCWT function.

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.

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.

See also

MSW for the standard user interface method. peakDetectionCWT from the MassSpecWavelet package.

Other core peak detection functions: do_findChromPeaks_centWave(), do_findChromPeaks_centWaveWithPredIsoROIs(), do_findChromPeaks_massifquant(), do_findChromPeaks_matchedFilter()

Author

Joachim Kutzera, Steffen Neumann, Johannes Rainer