[R] Newbie question

Chaser zhang816 at gmail.com
Wed Mar 26 19:56:03 CET 2008


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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