SignalProcessing: Signal processing for MALDI-TOF spectra (wrapper to SignalProcessingUltra)

Description

Backward-compatible wrapper that delegates to SignalProcessingUltra. Keeps the original argument names/signature so existing code continues to work.

Usage

SignalProcessing(
  x,
  transformIntensity_method = "sqrt",
  smoothing_method = "Wavelet",
  removeBaseline_method = "SNIP",
  removeBaseline_iterations = 25,
  calibrateIntensity_method = "TIC",
  alignSpectra_NoiseMethod = "MAD",
  alignSpectra_method = "lowess",
  alignSpectra_halfWs = 11,
  alignSpectra_SN = 3,
  tolerance_align = 0.002,
  referenceSpectra = NULL,
  minFrequency = 0.5,
  binPeaks_method = "strict",
  keepReferenceSpectra = FALSE,
  ...
)

Value

A list of processed MassSpectrum objects, or list(spectra, RefS) if keepReferenceSpectra = TRUE.

Arguments

x: list of MALDIquant MassSpectrum objects.
transformIntensity_method: character, intensity transform (default "log").
smoothing_method: character, smoothing method ("Wavelet" UDWT).
removeBaseline_method: character, baseline method ("TopHat" default; "SNIP","ConvexHull" supported).
removeBaseline_iterations: integer, SNIP iterations if removeBaseline_method = "SNIP".
calibrateIntensity_method: character, intensity calibration ("PQN" default, or "TIC","median").
alignSpectra_NoiseMethod: character, noise estimator for peak finding pre-alignment ("MAD").
alignSpectra_method: character, alignment engine: "cubic" (default), "lowess", or "landmark_cpp".
alignSpectra_halfWs: integer, half window size for peak detection.
alignSpectra_SN: numeric, SNR for peak detection.
tolerance_align: numeric, tolerance for matching anchors to the reference during alignment. Use consistent units across your pipeline (Da by default here).
referenceSpectra: optional MALDIquant MassPeaks object to use as alignment reference.
minFrequency: numeric, minimum peak frequency to build reference if not provided (default 0.7).
binPeaks_method: character, "strict" (default) or "relaxed" for reference peak binning.
keepReferenceSpectra: logical, if TRUE and no reference provided, returns list(spectra=..., RefS=...).
...: additional arguments passed to SignalProcessingUltra (e.g., n_workers, ref_sample_n).