This method smooths individual spectra (
or whole experiments (
Currently, the Savitzky-Golay-Smoothing (
method = "SavitzkyGolay")
and the Moving-Average-Smoothing (
method = "MovingAverage") are
available, as implemented in the
Additional methods might be added at a later stage.
signature(x = "MSnExp", method = "character", halfWindowSize = "integer", verbose = "logical", ...)
Smooths all spectra in
method could be
"halfWindowSize" controls the
window size of the filter. The resulting window size is
halfWindowSize + 1. The best size differs depending on the
method = "SavitzkyGolay" it
should be lower than FWHM of the peaks (full width at half
maximum; please find details in Bromba and Ziegler 1981). The
... are passed to the internal functions.
method="MovingAverage" there is an additional
FALSE) to indicate if the average should
be equal weight (default) or if it should have weights depending
on the distance from the center as calculated as
1/2^abs(-halfWindowSize:halfWindowSize) with the sum
of all weigths normalized to 1.
method="SavitzkyGolay" an additonal argument
polynomialOrder (default: 3). It controls the
polynomial order of the Savitzky-Golay Filter.
This method displays a progress bar if
verbose = TRUE.
MSnExp instance with smoothed spectra.
signature(x = "Spectrum", method = "character", halfWindowSize = "integer", ...)
Smooths the spectrum (
Spectrum instance). This method is
the same as above but returns a smoothed
MSnExp object. It has no
argument. Please read the details for the above
Sebastian Gibb <email@example.com>
A. Savitzky and M. J. Golay. 1964. Smoothing and differentiation of data by simplified least squares procedures. Analytical chemistry, 36(8), 1627-1639.
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/
sp1 <- new("Spectrum1", intensity = c(1:6, 5:1), mz = 1:11) sp2 <- smooth(sp1, method = "MovingAverage", halfWindowSize = 2) intensity(sp2) #>  3.0 3.0 3.0 4.0 4.6 4.8 4.6 4.0 3.0 3.0 3.0 data(itraqdata) itraqdata2 <- smooth(itraqdata, method = "MovingAverage", halfWindowSize = 2) processingData(itraqdata2) #> - - - Processing information - - - #> Data loaded: Wed May 11 18:54:39 2011 #> Updated from version 0.3.0 to 0.3.1 [Fri Jul 8 20:23:25 2016] #> Spectra smoothed (MovingAverage): Thu Sep 9 06:11:15 2021 #> MSnbase version: 1.1.22