back to emd() or dat() or some such then?

something shorter than values(foo)$bar would be handy.  I've switched to
using SummarizedExperiments for everything, so this isn't always as much of
a big deal as it once was, but for situations like Gviz, where internally
the code expects a GRanges with lots of stuff in the columns, it gets to be
a drag to write elementMetadata(foo)$bar all over the place.



On Fri, May 11, 2012 at 12:10 PM, Hervé Pagès <hpages@fhcrc.org> wrote:

> On 05/10/2012 03:22 PM, Tim Triche, Jr. wrote:
>
>> Incidentally, due to R's crappy unicode support, the € convention cannot
>> catch on...
>> I would have already patched it into GenomicRanges otherwise, just to run
>> with Herve's 4/1/2012 RFP.
>>
>> 'tis a shame, sort of.  After the EU breaks up, it will be a perfectly
>> good
>> operator symbol!
>>
>
> The € proposal was actually shortsighted... I heard rumors that
> our new president wants to get rid of the € key on French keyboards.
> The Germans don't like the idea.
>
> More seriously, values() for accessing the elementMetadata is a
> misnomer. Here is why: when we say that a vector or Vector 'x'
> "contains duplicated values", or that "its values are negative",
> or that "its values are unsorted" etc... or when we say that
> the 6-th value ('x[6]') is the max, and more generally when we
> talk about the i-th value in 'x', we refer to the naked 'x[i]'
> thing i.e. what remains after dropping the names, elementMetadata,
> and any possible attribute attached to it.
>
> More precisely: the comparison between 'x[i]' and 'x[j]' (i.e.
> the i-th and j-th *values* in 'x') ignores the attributes.
>
> For example, the *values* in GRanges object 'gr' are the genomic
> ranges. Each *value* in 'gr' is a quadruplet:
>
>  [seqname, strand, start, end]
>
> Any other stuff attached to a genomic range is not part of the
> value. Comparing 2 *values* in 'gr' is comparing 2 quadruplets
> i.e. it only looks at the seqname, strand, start, and end.
>
> So I'm all for getting rid of values() as an alias for
> elementMetadata(). If we want something shorter, fine, because
> it's an opportunity to get rid of it. But not v(), please.
>
> Cheers,
> H.
>
>
>>
>> On Thu, May 10, 2012 at 3:19 PM, Tim Triche, Jr.<tim.triche@gmail.com>**
>> wrote:
>>
>>  well, the obvious answer is to get rid of the function call :-D
>>>
>>> but that rather screws up the semantics of GRangesList so it's a
>>> nonstarter.
>>>
>>>
>>>
>>> On Thu, May 10, 2012 at 3:14 PM, Steve Lianoglou<
>>> mailinglist.honeypot@gmail.com**>  wrote:
>>>
>>>  On Thu, May 10, 2012 at 6:10 PM, Tim Triche, Jr.<tim.triche@gmail.com>
>>>> wrote:
>>>>
>>>>> Would anyone be opposed to this?
>>>>>
>>>>> I really prefer to have an expression on one line whenever possible,
>>>>> and
>>>>> when bolting things together with distanceToNearest and friends,
>>>>>
>>>> v(foo)$bar
>>>>
>>>>> <- baz is quite nice.
>>>>>
>>>>
>>>> Ironically, gmail broke up your oneliner preference example w/ a line
>>>> break :-)
>>>>
>>>> I'm not sure what type of omen that is for your proposal, but ...
>>>>
>>>> --
>>>> 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<http://cbio.mskcc.org/~lianos/contact>
>>>>
>>>>
>>>
>>>
>>> --
>>> *A model is a lie that helps you see the truth.*
>>> *
>>> *
>>> Howard Skipper<http://cancerres.**aacrjournals.org/content/31/9/**
>>> 1173.full.pdf<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>
>>> >
>>>
>>>
>>>
>>
>>
>>
>> ______________________________**_________________
>> Bioconductor mailing list
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>> Search the archives: http://news.gmane.org/gmane.**
>> science.biology.informatics.**conductor<http://news.gmane.org/gmane.science.biology.informatics.conductor>
>>
>
>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>



-- 
*A model is a lie that helps you see the truth.*
*
*
Howard Skipper<http://cancerres.aacrjournals.org/content/31/9/1173.full.pdf>

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