Peak detection of mass spectrum by Wavelet transform based methods

Description

Process Mass Spectrum (MS) by Wavelet Transforms-based algorithms

Details

MassSpecWavelet R package is aimed to process Mass Spectrometry (MS) data mainly based on Wavelet Transforms. The current version only supports the peak detection based on Continuous Wavelet Transform (CWT). Future versions will include more functions covering entire MS data processes.

Author(s)

Pan Du, Simon Lin

Maintainer: Pan Du <dupan@northwestern.edu>

References

Du, P., Kibbe, W.A. and Lin, S.M. (2006) Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching, Bioinformatics, 22, 2059-2065.

Examples

data(exampleMS)
SNR.Th <- 3
peakInfo <- peakDetectionCWT(exampleMS, SNR.Th=SNR.Th)
majorPeakInfo = peakInfo$majorPeakInfo
peakIndex <- majorPeakInfo$peakIndex
plotPeak(exampleMS, peakIndex, main=paste('Identified peaks with SNR >', SNR.Th)) 

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(MassSpecWavelet)
Loading required package: waveslim

waveslim: Wavelet Method for 1/2/3D Signals (version = 1.7.5)

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MassSpecWavelet/MassSpecWavelet.package.Rd_%03d_medium.png", width=480, height=480)
> ### Name: MassSpecWavelet-package
> ### Title: Peak detection of mass spectrum by Wavelet transform based
> ###   methods
> ### Aliases: MassSpecWavelet-package MassSpecWavelet
> ### Keywords: package
> 
> ### ** Examples
> 
> data(exampleMS)
> SNR.Th <- 3
> peakInfo <- peakDetectionCWT(exampleMS, SNR.Th=SNR.Th)
> majorPeakInfo = peakInfo$majorPeakInfo
> peakIndex <- majorPeakInfo$peakIndex
> plotPeak(exampleMS, peakIndex, main=paste('Identified peaks with SNR >', SNR.Th)) 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>