[BioC] c()ombining G/IRanges with elementMetadata: feature inquiry/request

[Steve Lianoglou]

On Mon, Feb 7, 2011 at 2:58 PM, Martin Morgan <mtmorgan at fhcrc.org> wrote:
> On 02/07/2011 10:36 AM, Steve Lianoglou wrote:
>> On Mon, Feb 7, 2011 at 1:08 PM, Michael Lawrence
>> <lawrence.michael at gene.com> wrote:
>>> On Mon, Feb 7, 2011 at 9:42 AM, Steve Lianoglou
>>> <mailinglist.honeypot at gmail.com> wrote:
[snip]
>> I'm curious what the folks at The Hutch had in mind with respect to
>> how they envisioned the `elementMetadata` vs. `values` api to play
>> out?
>
> 'values' for GenomicRanges.

Ok ... obviously it's your decision to make, but isn't it a bit
confusing to settle on values() for GenomicRanges objects and
elementMetadata() for IRanges when both "things" represent the same
"thing"? What's the motivation for that?

>>> But yea, your idea for 'c' is convenient. Care to submit a patch?
>>
>> I'd be happy to ... maybe just as soon as we get a green light from
>> The Hutch (w.r.t utility and param. name)?
>
> yes sounds good.

Given the values vs. elementMetadata thing above, what should the
appropriate name for the parameter be that we're talking about here?

Would the c,GenomicRanges function then have a different name for this
parameter (.ignoreValues) as compared and to the c,IRanges(or anything
else) (.ignoreElementMetadata)?

> Is this what 'recursive' is supposed to regulate (with
> the current behavior recursive = TRUE, despite the signature?).

I'm not sure. I'm having a hard time imagining how recursive=TRUE vs.
FALSE would actually behave in the c()-context.

Maybe it would make more sense to check for it to be !missing then
give a warning telling the user it's not being handled, eg:

if (!missing(recursive)) {
  warning("`recursive` parameter is ignored ...")
}

(or some such)

> I'm
> recognizing the more-or-less fractal nature of IRanages, and the
> multiple elementMetadata locations in GRanges (on ranges(), on values(),
> as well as values(ranges()), values(values()), etc.)

I never thought about the values() of the ranges() of a GenomicRanges
object actually ...

While we're at it, I guess there should be a "values" method defined
in GenomicRanges that just aliases its elementMetadata() function:

setMethod("values", "GenomicRanges", function(x, ...) elementMetadata(x, ...)

since elementMetadata,GenomicRanges does some `rownames` bookkeeping
before it passes down to the elementMetadata,Sequence method.

Thanks,
-steve

-- 
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