smooth-methods: Smooths 'MSnExp' or 'Spectrum' instances

In MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

Description

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(s)

Sebastian Gibb <[e-mail]>

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/

See Also

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

Examples

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)

MSnbase documentation built on Jan. 23, 2021, 2 a.m.