estimateNoise-methods {MSnbase} | R Documentation

## 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/

### See Also

`pickPeaks`, and the underlying method in `MALDIquant`: `estimateNoise`.

### Examples

    sp1 <- new("Spectrum1",
               intensity = c(1:6, 5:1),
               mz = 1:11,
               centroided = FALSE)
    estimateNoise(sp1, method = "SuperSmoother")

[Package MSnbase version 2.20.1 Index]