Spectrum instances)
or whole experiments (MSnExp instances).
Currently, the Savitzky-Golay-Smoothing (method = "SavitzkyGolay")
and the Moving-Average-Smoothing (method = "MovingAverage") are
available, as implemented in the MALDIquant::smoothIntensity function.
Additional methods might be added at a later stage.
signature(x = "MSnExp", method = "character",
halfWindowSize = "integer", verbose = "logical", ...)MSnExp. method could be
"SavitzkyGolay" or "MovingAverage}. \code{halfWindowSize}
controls the window size of the filter. The resulting window size is
\code{2 * halfWindowSize + 1}. The best size differs depending on
the selected \code{method}. For \code{method = "SavitzkyGolay"} it
should be lower than \emph{FWHM} of the peaks (full width
at half maximum; please find details in Bromba and Ziegler 1981).
The arguments \code{\dots} are passed to the internal functions.
Currently the only supported argument is \code{polynomialOrder}
(default: 3) for \code{method="SavitzkyGolay to control the
polynomial order of the Savitzky-Golay Filter.
This method displays a progress bar if verbose = TRUE.
Returns an MSnExp instance with smoothed spectra.
signature(x = "Spectrum", method = "character",
halfWindowSize = "integer", ...)Spectrum instance). This method is the same
as above but returns a smoothed Spectrum instead of an
MSnExp object. It has no verbose argument. Please read the
details for the above MSnExp method.
M. U. Bromba and H. Ziegler. 1981. Application hints for Savitzky-Golay digital smoothing filters. Analytical Chemistry, 53(11), 1583-1586.
S. Gibb and K. Strimmer. 2012. MALDIquant: a versatile R package for the analysis of mass spectrometry data. Bioinformatics 28: 2270-2271. http://strimmerlab.org/software/maldiquant/
clean, pickPeaks, removePeaks and
trimMz for other spectra processing methods.
sp1 <- new("Spectrum1",
intensity = c(1:6, 5:1),
mz = 1:11)
sp2 <- smooth(sp1, method = "MovingAverage", halfWindowSize = 2)
intensity(sp2)
data(itraqdata)
itraqdata2 <- smooth(itraqdata,
method = "MovingAverage",
halfWindowSize = 2)
processingData(itraqdata2)
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