Noise Estimation for 'Spectrum' instances

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

Sebastian Gibb <mail@sebastiangibb.de>

See also

pickPeaks, and the underlying method in MALDIquant: estimateNoise.

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")
#>       mz intensity
#>  [1,]  1      1.08
#>  [2,]  2      2.00
#>  [3,]  3      2.92
#>  [4,]  4      3.68
#>  [5,]  5      4.20
#>  [6,]  6      4.40
#>  [7,]  7      4.20
#>  [8,]  8      3.68
#>  [9,]  9      2.92
#> [10,] 10      2.00
#> [11,] 11      1.08