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 signature 'MassSpectrum'
estimateNoise(object,
  method=c("MAD", "SuperSmoother"),
  ...)

Arguments

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.

Value

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

Author(s)

Sebastian Gibb mail@sebastiangibb.de

See Also

MassSpectrum, detectPeaks,MassSpectrum-method, mad, supsmu

Website: http://strimmerlab.org/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))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(MALDIquant)

This is MALDIquant version 1.15
Quantitative Analysis of Mass Spectrometry Data
 See '?MALDIquant' for more information about this package.

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/MALDIquant/estimateNoise-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: estimateNoise-methods
> ### Title: Estimates the noise of a MassSpectrum object.
> ### Aliases: estimateNoise estimateNoise,MassSpectrum-method
> ### Keywords: methods
> 
> ### ** 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))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>