[Bioc-devel] RangedSummarizedExperiment

Elena Grassi grassi.e at gmail.com
Thu Jun 18 19:48:43 CEST 2015

Hi Hervé,

thanks for your kind answer - refactoring is always good, I've lagged
behind in the last months not following the novelties so to be
truthful it has been my fault and today I was in a bit of a hurry for
other reasons.

> I'm in the process of re-serializing
> RangedSummarizedExperiment objects and fixing the packages affected
> by these changes (should be done before the end of the week).

Yup, I see. roar should be fixed now even if I'm not sure that the
solution is satisfying in the long run, maybe after the bulk
refactoring of SummarizedExperiment comes to an end I will reconsider
some refactoring too :)
Thanks for the explanations they cleared my head around some issues!

>> - it would be better to avoid extending such a class and instead
>> simply having another slot to avoid such initializations issues?
> Not sure I understand what you're asking exactly. Can you provide
> more details?

That wasn't a very clear question also in my mind, sorry...it derived
from my not so deep understanding of S4 inheritance mechanism, I tried
to patch it today :)
Basically I was wondering if extending classes and thus maybe
tinkering with their inner mechanisms more than when simply composing
would be considered a better practice in Bioconductor where the API
are not always stable but looking around in the codebase convinced me
that it it's not the case.

Thanks again,

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