estimateNoise-method.Rd
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.
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
.
pickPeaks
, and the underlying method in MALDIquant
:
estimateNoise
.
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/
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