Access to Source Codes of Packges
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Karthik K N ▴ 200
@karthik-k-n-5092
Last seen 8.3 years ago
Hello members, I am using AgiMicroRna and Limma packges for analyzing Agilent microarray data. I would like to know if it is possible to have access to the source codes of these packages so that I can better understand what is goind on in the background when we call each functions. Also, is it possible to edit the source code and run the package? Thanks a lot in advance, Regards, -- Karthik [[alternative HTML version deleted]]
limma AgiMicroRna limma AgiMicroRna • 2.2k views
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@sean-davis-490
Last seen 3 months ago
United States
On Sat, Jun 16, 2012 at 6:19 AM, Karthik K N <karthikuttan at="" gmail.com=""> wrote: > Hello members, > > I am using AgiMicroRna and Limma packges for analyzing Agilent microarray > data. I would like to know if it is possible to have access to the source > codes of these packages so that I can better understand what is goind on in > the background when we call each functions. Yes. The source code is available from the website. Just find the package you like and download the source code. Alternatively, the SVN repository for bioconductor is open. See the developer section of the website for how to access it. > Also, is it possible to edit the source code and run the package? Yes. You'll want to read at least some sections of the "Writing R Extensions" manual available from CRAN (or a mirror). Sean > > Thanks a lot in advance, > > Regards, > > -- > Karthik > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Karthik K N ▴ 200
@karthik-k-n-5092
Last seen 8.3 years ago
Dear David, Thank you for your help. Can you please tell me how do you exactly edit the source code of a package and the use this 'modified package'? For example, I was wondering if it is possible to add some 'filter by flags' option in limma so that I can filter out probes that do not meet the specified flag criteria from my Agilent single color microarray data set ( I am not sure if limma already has this function). Is this possible in limma? Thanks, Karthik On Sat, Jun 16, 2012 at 4:06 PM, David Westergaard <david@harsk.dk> wrote: > Dear Karthik, > > If you go to the Bioconductor website www.bioconductor.org), and > search for a package, (e.g. limma: > http://www.bioconductor.org/packages/release/bioc/html/limma.html), at > the very bottom you have to option to download the source. If you are > just curious as to how the code looks, you can also view the source by > calling the function without any parameters. For instance, just > running 'lmFit' would return the functions source code. > > Yes, it is also possible to edit the source code. > > Best, > David > > 2012/6/16 Karthik K N <karthikuttan@gmail.com>: > > Hello members, > > > > I am using AgiMicroRna and Limma packges for analyzing Agilent microarray > > data. I would like to know if it is possible to have access to the source > > codes of these packages so that I can better understand what is goind on > in > > the background when we call each functions. > > > > Also, is it possible to edit the source code and run the package? > > > > Thanks a lot in advance, > > > > Regards, > > > > -- > > Karthik > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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On Sat, Jun 16, 2012 at 6:50 AM, Karthik K N <karthikuttan at="" gmail.com=""> wrote: > Dear David, > > Thank you for your help. Can you please tell me how do you exactly edit the > source code of a package and the use this 'modified package'? You simply download the source code, open up the relevant files (you have to know which those are) with any text editor you like, edit what you like, test your new code and install the edited package. You'll need to do some homework on this, though. > For example, I was wondering if it is possible to add some 'filter by > flags' option in limma so that I can filter out probes that do not meet the > specified flag criteria from my Agilent single color microarray data set ( > I am not sure if limma already has this function). Is this possible in > limma? This is already possible with limma/bioconductor, but you can certainly change limma to your heart's content if you have an idea on how to improve things for your own use. That is the wonder of open source and development. Sean > On Sat, Jun 16, 2012 at 4:06 PM, David Westergaard <david at="" harsk.dk=""> wrote: > >> Dear Karthik, >> >> If you go to the Bioconductor website www.bioconductor.org), and >> search for a package, (e.g. limma: >> http://www.bioconductor.org/packages/release/bioc/html/limma.html), at >> the very bottom you have to option to download the source. If you are >> just curious as to how the code looks, you can also view the source by >> calling the function without any parameters. For instance, just >> running 'lmFit' would return the functions source code. >> >> Yes, it is also possible to edit the source code. >> >> Best, >> David >> >> 2012/6/16 Karthik K N <karthikuttan at="" gmail.com="">: >> > Hello members, >> > >> > I am using AgiMicroRna and Limma packges for analyzing Agilent microarray >> > data. I would like to know if it is possible to have access to the source >> > codes of these packages so that I can better understand what is goind on >> in >> > the background when we call each functions. >> > >> > Also, is it possible to edit the source code and run the package? >> > >> > Thanks a lot in advance, >> > >> > Regards, >> > >> > -- >> > Karthik >> > >> > ? ? ? ?[[alternative HTML version deleted]] >> > >> > _______________________________________________ >> > Bioconductor mailing list >> > Bioconductor at r-project.org >> > https://stat.ethz.ch/mailman/listinfo/bioconductor >> > Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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