[R] Simple problem in R
I found a package on www.bioconductor.com that allows me to install using
this line:
source("http://bioconductor.org/biocLite.R";)
biocLite("MassSpecWavelet")
The prompt showed me the following message:
Running biocinstall version 2.1.10 with R version 2.6.2
Your version of R requires version 2.1 of Bioconductor.
trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/MassSpecWavelet_1.4.0.zip'
Content type 'application/zip' length 2129961 bytes (2.0 Mb)
opened URL
downloaded 2.0 Mb
package 'MassSpecWavelet' successfully unpacked and MD5 sums checked
The downloaded packages are in
C:\Documents and Settings\Yuan\Local
Settings\Temp\RtmpIjgEwP\downloaded_packages
updating HTML package descriptions
In their help package, they have listed commands that will allow a sample
runthrough of their algorithm using a sample dataset.
I entered these codes in but was returned the following error messages:
data(exampleMS)
Warning message:
In data(exampleMS) : data set 'exampleMS' not found
> SNR.Th <- 3
> peakInfo <- peakDetectionCWT(exampleMS, SNR.Th=SNR.Th)
Error: could not find function "peakDetectionCWT"
> majorPeakInfo = peakInfo$majorPeakInfo
Error: object "peakInfo" not found
> peakIndex <- majorPeakInfo$peakIndex
Error: object "majorPeakInfo" not found
> plotPeak(exampleMS, peakIndex, main=paste('Identified peaks with SNR >',
> SNR.Th))
Did I make a mistake somewhere or is the code they wrote flawed?
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Re: [R] Simple problem in R
I never knew to enter that command in. Thanks guys! -- View this message in context: http://www.nabble.com/Simple-problem-in-R-tp16259116p16260713.html Sent from the R help mailing list archive at Nabble.com. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] Newbie question
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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and provide commented, minimal, self-contained, reproducible code.
