[R] Newbie question

From: Chaser <zhang816_at_gmail.com>
Date: Wed, 26 Mar 2008 11:56:03 -0700 (PDT)

Hey everyone,

For my research, I needed a peak detector algorithm that can spot peaks in an intensity graph. The excel
http://www.nabble.com/file/p16313309/sample%2Bdata.xls sample data that I've attached contains columns of such intensity graphs.

I came found an algorithm developed by the http://www.bioconductor.com Bioconductor team and was excited to test it out on my own data. However, it is written in R. With my own programming experience being Matlab and having little experience with programming to begin with, I've hit a bit of a road block and need whatever help you guys can offer.

I need to run my data through this algorithm and see what kind of peaks are detected. How do I format my excel data to a .rda format that the algorithm can work with?

The algorithm can be found
http://www.bioconductor.org/packages/bioc/html/MassSpecWavelet.html here .

To load the package, enter:

source("http://bioconductor.org/biocLite.R") biocLite("MassSpecWavelet")
library(MassSpecWavelet)

The package comes with a sample data that is VERY similar to my own data (which is why I think it will work for my project)

To load the packaged example data and see what the package does, enter:

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))

Any help you guys can offer will be greatly appreciated.

Thanks!

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