MALDIquant (version 1.22.3)

estimateNoise-methods: Estimates the noise of a MassSpectrum object.

Description

This method estimates the noise of mass spectrometry data (represented by a MassSpectrum object).

Usage

# S4 method for MassSpectrum
estimateNoise(object,
  method=c("MAD", "SuperSmoother"),
  ...)

Value

Returns a two column matrix (first column: mass, second column: intensity) of the estimated noise.

Arguments

object

MassSpectrum object

method

used noise estimation method, one of "MAD" or "SuperSmoother".

...

arguments to be passed to method.

Author

Sebastian Gibb

Details

"MAD":

This function estimates the noise of mass spectrometry data by calculating the median absolute deviation, see also mad.

"SuperSmoother":

This function estimates the noise of mass spectrometry data using Friedman's Super Smoother. Please refer supsmu for details and additional arguments.

See Also

MassSpectrum, detectPeaks,MassSpectrum-method, mad, supsmu

Website: https://strimmerlab.github.io/software/maldiquant/

Examples

## load package
library("MALDIquant")

## load example data
data("fiedler2009subset", package="MALDIquant")

## choose only the first mass spectrum
s <- fiedler2009subset[[1]]

## transform intensities
s <- transformIntensity(s, method="sqrt")

## remove baseline
s <- removeBaseline(s)

## plot spectrum
plot(s)

## estimate noise
nm <- estimateNoise(s, method="MAD")
nss <- estimateNoise(s, method="SuperSmoother")

## draw noise on the plot
lines(nm, col=2)
lines(nss, col=4)

## draw legend
legend(x="topright", lwd=1, legend=c("MAD", "SuperSmoother"),
       col=c(2, 4))