wavSmoothing {MALDIrppa}R Documentation

Discrete wavelet transformation for MassSpectrum objects

Description

This function performs undecimated wavelet transform (UDWT) on mass spectra in MassSpectrum format. Alternatively, smoothing methods included in the MALDIquant package can be called.

Usage

wavSmoothing(x, method = c("Wavelet", "SavitzkyGolay", "MovingAverage"),
             thresh.scale = 2.5, ...)

Arguments

x

A list of MassSpectrum objects.

method

Smoothing method used.

thresh.scale

Smoothing factor for wavelet-based smoothing.

...

Other arguments.

Details

The Wavelet method relies on the wavShrink function of the wmtsa package and its dependencies (now archived by CRAN). The original C code by William Constantine and Keith L. Davidson, in turn including copyrighted routines by Insightful Corp., has been revised and included into MALDIrppa for the method to work. Alternatively, smoothing methods SavitzkyGolay and MovingAverage from the MALDIquant package can be called directly from the function.

Value

A list of MassSpectrum objects with denoised signal intensities.

Examples

# Load example data

data(spectra) # list of MassSpectra class objects

# sqrt transformation and signal smoothing using UDWT

spectra <- transformIntensity(spectra, method = "sqrt")
spectra <- wavSmoothing(spectra)

[Package MALDIrppa version 1.0.5-1 Index]