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Smooths 'MSnExp' or 'Spectrum' instances

smooth-methods.Rd

This 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.

Methods

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.

Author

Sebastian Gibb <mail@sebastiangibb.de>

See also

clean, pickPeaks, removePeaks and trimMz for other spectra processing methods.

References

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/

Examples

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): Tue Oct 15 15:27:24 2024 
#>  MSnbase version: 1.1.22