MSnbase: estimateNoise-method – R documentation

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estimateNoise-method

Noise Estimation for 'Spectrum' instances

Description

This method performs a noise estimation on individual spectra (Spectrum instances). There are currently two different noise estimators, the Median Absolute Deviation (method = "MAD") and Friedman's Super Smoother (method = "SuperSmoother"), as implemented in the MALDIquant::detectPeaks and MALDIquant::estimateNoise functions respectively.

Methods

signature(object = "Spectrum", method = "character", ...): Estiamtes the noise in a non-centroided spectrum (Spectrum instance). method could be "MAD" or "SuperSmoother". The arguments ... are passed to the noise estimator functions implemented in MALDIquant::estimateNoise. Currenlty only the method = "SuperSmoother" accepts additional arguments, e.g. span. Please see supsmu for details. This method returns a two-column matrix with the m/z and intensity values in the first and the second column.
signature(object = "MSnExp", method = "character", ...): Estimates noise for all spectra in object.

Author(s)

Sebastian Gibb <mail@sebastiangibb.de>

References

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,
           centroided = FALSE)
estimateNoise(sp1, method = "SuperSmoother")

MSnbase

Base Functions and Classes for Mass Spectrometry and Proteomics

v2.16.1

Artistic-2.0

Authors

Laurent Gatto, Johannes Rainer and Sebastian Gibb with contributions from Guangchuang Yu, Samuel Wieczorek, Vasile-Cosmin Lazar, Vladislav Petyuk, Thomas Naake, Richie Cotton, Arne Smits, Martina Fisher, Ludger Goeminne, Adriaan Sticker and Lieven Clement.

Initial release