smooth-methods {MSnbase} | R Documentation

## Smooths 'MSnExp' or 'Spectrum' instances

### 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 <mail@sebastiangibb.de>

### 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)

[Package MSnbase version 2.20.1 Index]