smoothIntensity-methods: Smoothes intensities of a MassSpectrum object.

Description

This method smoothes the intensity values of a MassSpectrum object.

Usage

## S3 method for class 'MassSpectrum':
smoothIntensity(object,
  method=c("SavitzkyGolay", "MovingAverage"), halfWindowSize,
  ...)

Arguments

object

AbstractMassObject object or a list of AbstractMassObject objects.

method

used smoothing method, one of "SavitzkyGolay" or "MovingAverage".

halfWindowSize

half window size. The resulting window reaches from mass[currentIndex-halfWindowSize] to mass[currentIndex+halfWindowSize] (window size is 2*halfWindowSize+1). The best size differs depending on the

...

arguments to be passed to method. SavitzkyGolay has an additional polynomialOrder argument (default: 3) to control the order of the filter. Unused for MovingAverage

Details

halfWindowSize: Depends on the selected method. For the SavitzkyGolay the halfWindowSize should be smaller than FWHM of the peaks (full width at half maximum; please find details in Bromba and Ziegler 1981). In general the halfWindowSize for the MovingAverage has to be much smaller than for SavitzkyGolay to conserve the peak shape.

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.

Examples

Run this code

## load package
library("MALDIquant")

## load example data
data("fiedler2009subset", package="MALDIquant")

## smooth spectra
s <- smoothIntensity(fiedler2009subset, method="MovingAverage",
                     halfWindowSize=2)
## or
s <- smoothIntensity(fiedler2009subset, method="SavitzkyGolay",
                     halfWindowSize=10)