[BioC] Access to Source Codes of Packges

[Sean Davis]

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]]
>> >
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