## alignSpectra
## wrapper around detectPeaks, determineWarpingFunctions and warpMassSpectra
##
## params:
## spectra: list, list of MassSpectrum objects
## halfWindowSize: numeric, half window size.
## noiseMethod: character, noise estimation method
## SNR: double, signal-to-noise ratio
## reference: MassPeaks, a reference MassPeaks object to which all other
## MassPeaks objects should be aligned
## tolerance: double, maximal deviation of a peak position to be
## considered as same peak
## warpingMethod: choose type of base warping function
## allowNoMatches: logical, don't throw an error if a single MassPeaks object
## could not match to the reference.
## emptyNoMatches: logical, if TRUE mismatches (warping function NA)
##
## returns:
## a list of aligned MassSpectrum objects
##
alignSpectra <- function(spectra,
## peak detection
halfWindowSize=20, noiseMethod="MAD", SNR=2,
## warping
reference, tolerance=0.002, warpingMethod="lowess",
allowNoMatches=FALSE, emptyNoMatches=FALSE, ...) {
## test arguments
.stopIfNotIsMassSpectrumList(spectra)
peaks <- detectPeaks(spectra, halfWindowSize=halfWindowSize,
method=noiseMethod, SNR=SNR, ...)
wf <- determineWarpingFunctions(peaks, reference=reference,
tolerance=tolerance, method=warpingMethod,
allowNoMatches=allowNoMatches)
warpMassSpectra(spectra, wf, emptyNoMatches=emptyNoMatches)
}
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