[BioC] Bioconductor, naming of functions

[Martin Morgan]

Hi Markus --

Sometimes we're stuck with what went before, for better or worse.

A '.'  in a function name _does_ have a special meaning (in the 'S3'
object system, section 10.9 of 'An Introduction To R', for
detail). Unfortunately, the dot in just.rma is not being used in that
way, and the Bioconductor project emphasizes the S4 rather than S3
object system. With hindsight a better name would have been along the
lines of justRma. A dot in the function name only causes confusion,
and should be avoided.

Questions like this might be better on the Bioc-devel list, though
they're welcome anywhere!

Martin

Markus Schmidberger <schmidb at ibe.med.uni-muenchen.de> writes:

> Hello
>
> I was reading the guidelines at the bioconductor developer page. But how 
> about naming functions?
> There is a part for "variable names" and the hint for using namespaces. 
> In several packages I found functions of the kind: "just.rma"
> Is using the "dot" in a function name permitted and has the "dot" any 
> meaning?
>
> Thanks
> Markus
>
> -- 
> Dipl.-Tech. Math. Markus Schmidberger
>
> Ludwig-Maximilians-Universität München
> IBE - Institut für medizinische Informationsverarbeitung,
> Biometrie und Epidemiologie
> Marchioninistr. 15, D-81377 Muenchen
> URL: http://ibe.web.med.uni-muenchen.de 
> Mail: Markus.Schmidberger [at] ibe.med.uni-muenchen.de
>
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org