smooth-methods.RdThis method smooths individual spectra (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", ...)Smooths all spectra in MSnExp. method could be
"SavitzkyGolay" or
"MovingAverage". "halfWindowSize" controls the
window size of the filter. The resulting window size is 2 *
halfWindowSize + 1. The best size differs depending on the
selected method. For 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
arguments ... are passed to the internal functions.
For method="MovingAverage" there is an additional weighted
argument (default: 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.
For method="SavitzkyGolay" an additonal argument
is polynomialOrder (default: 3). It controls 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", ...)Smooths the spectrum (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.
clean, pickPeaks, removePeaks and
trimMz for other spectra processing methods.
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)
#> [1] 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 Mar 14 06:11:49 2024
#> MSnbase version: 1.1.22