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Last data update: 2014.03.03

R: Detects peaks in a MassSpectrum object.

detectPeaks-methods

R Documentation

Detects peaks in a MassSpectrum object.

Description

This method looks for peaks in mass spectrometry data (represented by a MassSpectrum object).
A peak is a local maximum above a user defined noise threshold.

Usage

## S4 method for signature 'MassSpectrum'
detectPeaks(object,
  halfWindowSize=20, method=c("MAD", "SuperSmoother"), SNR=2,
  ...)
## S4 method for signature 'list'
detectPeaks(object, ...)

Arguments

`object`	`MassSpectrum` object or a `list` of `MassSpectrum` objects.
`halfWindowSize`	`numeric`, half window size. The resulting window reaches from `mass[currentIndex-halfWindowSize]` to `mass[currentIndex+halfWindowSize]`. A local maximum have to be the highest one in the given window to be recognized as peak.
`method`	a noise estimation function; see `estimateNoise,MassSpectrum-method`.
`SNR`	single numeric value. `SNR` is an abbreviation for signal-to-noise-ratio. A local maximum has to be higher than `SNR*noise` to be recognize as peak.
`...`	arguments to be passed to `estimateNoise,MassSpectrum-method`. If `object` is a `list` `mc.cores` is also supported.

Value

Returns a MassPeaks object.

Author(s)

Sebastian Gibb mail@sebastiangibb.de

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")

## smoothing spectrum
s <- smoothIntensity(s, method="MovingAverage")

## remove baseline
s <- removeBaseline(s)

## plot spectrum
plot(s)

## call peak detection
p <- detectPeaks(s)

## draw peaks on the plot
points(p)

## label 10 highest peaks
top10 <- intensity(p) %in% sort(intensity(p), decreasing=TRUE)[1:10]
labelPeaks(p, index=top10)

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/detectPeaks-methods.Rd_%03d_medium.png", width=480, height=480)
> ### Name: detectPeaks-methods
> ### Title: Detects peaks in a MassSpectrum object.
> ### Aliases: detectPeaks detectPeaks,MassSpectrum-method
> ###   detectPeaks,list-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")
> 
> ## smoothing spectrum
> s <- smoothIntensity(s, method="MovingAverage")
> 
> ## remove baseline
> s <- removeBaseline(s)
> 
> ## plot spectrum
> plot(s)
> 
> ## call peak detection
> p <- detectPeaks(s)
> 
> ## draw peaks on the plot
> points(p)
> 
> ## label 10 highest peaks
> top10 <- intensity(p) %in% sort(intensity(p), decreasing=TRUE)[1:10]
> labelPeaks(p, index=top10)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>