[BioC] Performing set ops with an IRanges object loaded with elementMetadata is like a shotgun, pointing at my foot.

[Steve Lianoglou]

On Mon, Jul 12, 2010 at 2:49 PM, Michael Lawrence
<lawrence.michael at gene.com> wrote:
> On Mon, Jul 12, 2010 at 11:05 AM, Steve Lianoglou
> <mailinglist.honeypot at gmail.com> wrote:
<snip>
>> I don't know what the answer *really* should be as to what the correct
>> behavior in this situation would be, which I guess could be an
>> interesting discussion ... perhaps the elementMetadata can be
>> split/merged with its associated range, or just dropped all together
>> (perhaps via some explicit parameter in the setdiff, etc. function
>> call?).
>>
>> Anyway, in an effort to skirt that rabbit hole for now, could I ask
>> for a feature request and have IRanges provide a more informative
>> error message when an end user is gunning at their feet w/ this
>> scenario? :-)
>>
>
> I think it would be reasonable to simply drop the metadata, since one is
> creating an entirely new set of ranges. Might want a warning/message, but
> I'm not sure if even that is necessary. Just need to document the behavior.

I agree that dropping the metadata is sufficient, but (if we were
taking a vote) I think I'd have a slight (+0) preference for it to
fire off a warning if any of the IRanges objects had metadata that was
dropped.

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact