[Bioc-devel] A new beginner

Stefano Calza stefano.calza at med.unibs.it
Thu Feb 17 15:34:47 CET 2011


you probably mean you have been programming using S3 methods not S4.

Using S4 methods is not compulsory though highly recommended. At least this is my understanding. There are packages in BioC not using S4, therefore I assume you can go ahead like this.

Most packages in BioC use S4 methods, so just pick one not too complex!



On Thu, Feb 17, 2011 at 02:17:31PM +0000, Stefano Berri wrote:
<Stefano>Hi everybody.
<Stefano>I am about to start assembling my code to make my first Bioconductor
<Stefano>I've read the instructions about "Package Guidelines" and "Package
<Stefano>Submission" and I will try to follow those instruction the best I can.
<Stefano>I have a first question, however.
<Stefano>You seem to ask for your code to be in S4 Classes and Methods
<Stefano>( Packages should also conform to the following:
<Stefano>* Use S4 classes and methods.)
<Stefano>At the moment I wrote my code in the form
<Stefano>List <- myFunction(List, bar = bar, foo = foo)
<Stefano>Using "plain functions" and Lists as input and output.
<Stefano>I was inspired by 'limma' that, as far as I understand, works this way.
<Stefano>Can submit using this interface or shall I really use S4 implementation? If
<Stefano>so, could you recommend a simple package that uses classes as you would
<Stefano>recomend that I can use as template/inspration/guide for my code?
<Stefano>Thank you very much
<Stefano>Stefano Berri
<Stefano>Bioc-devel at r-project.org mailing list

Stefano Calza, PhD
Ricercatore (Assistant Professor) - Biostatistician
*Sezione di Statistica Medica e Biometria
 Dipartimento di Scienze Biomediche e Biotecnologie
 Università degli Studi di Brescia - Italy
 Viale Europa, 11 25123 Brescia

 email: stefano.calza at med.unibs.it
        stefano.calza at biostatistics.it

 pec: stefano.calza at pec.biostatistics.it

 Phone: +390303717653
 Fax: +390303717488


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