Right around the time I get used to using values(GR) all over the place...
and, an excellent opportunity to improve R's Unicode support, squandered!
 ;-)

As long as things work right for SummarizedExperiments and their coercions
to/from other common data structures, I'm certainly not going to complain.
I'm not sure how I feel about having urged Hervé and Martin to compromise
their principles about this, but it will make some peoples' lives a lot
easier.
Not least, mine, as I try to get examples and documentation completed for
the 'regulatoR' package I've been working on lately.

Having seen the logic behind your original design decisions, I understand
why you were reluctant to do this.
If it turns out that we have demanded "enough rope to shoot ourself in the
foot", well, we asked for it!
So, thank you, quite a lot, for including something that could well be as
dangerous as it is handy.

Thanks,

--t


On Thu, Aug 16, 2012 at 10:44 AM, Hervé Pagès <hpages@fhcrc.org> wrote:

> Hi Michael,
>
>
> On 08/16/2012 10:25 AM, Michael Lawrence wrote:
>
>>
>>
>> On Thu, Aug 16, 2012 at 10:16 AM, Hervé Pagès <hpages@fhcrc.org
>> <mailto:hpages@fhcrc.org>> wrote:
>>
>>     Hi,
>>
>>     People generally ask "do you want me to start with the good or with
>>     the bad news?" Here they are in no particular order (both are changes
>>     in BioC devel):
>>
>>     - I've added the mcols() accessor as the preferred way (over
>>        elementMetadata() and values()) to access the metadata columns.
>>        Also the term "metadata columns" is now used consistently
>>        everywhere in the IRanges/GenomicRanges/__**Rsamtools
>> documentation
>>
>>        (instead of "element metadata", "elementMetadata columns",
>>        "values", "columns of values", "metadata values",
>>        "elementMetadata values", etc...)
>>
>>
>>
>> I am wondering about the name choice. What about "metaframe"? That way
>> it is similar to the analogous but differently shaped "metadata" and
>> conveys the nature of the return value.
>>
>
> The name of the accessor should be consistent with the english term we
> use in emails or in the documentation. I don't remember anybody
> referring to the metadata columns as the "meta frame" or the
> "metadata frame". Beside "mcols" is shorter than "metaframe".
>
>
>
>>
>>        Having 3 synonyms for accessing the same thing is of course not
>>        ideal but I hope we can remedy this in the future.
>>
>>     - I've added "$" and "$<-" methods for GRanges *only*. Provided
>>        as a convenience and as the result of strong popular demand. Note
>>        that those methods are not consistent with the other "$" and "$<-"
>>        methods defined in the IRanges/GenomicRanges infrastructure, and
>>        might confuse some users by making them believe that a GRanges
>>        object can be manipulated as a data.frame-like object. It is
>>        therefore recommended to use them only interactively, and
>>        their use in scripts or packages is discouraged (in that
>>        case, 'mcols(x)$name' should be used instead of 'x$name').
>>
>>
>> Awesome. So it is now time to begin the campaign for adding this to
>> GRangesList, since people will be confused about the inconsistency
>> between the very similar (often interchangeable) data structures.
>>
>>
> "$" is already implemented for GRangesList and does the right thing.
>
> Cheers,
> H.
>
>  Thanks for the update (where was the bad news?),
>> Michael
>>
>>     Those changes are in IRanges 1.15.35 and GenomicRanges 1.9.48.
>>     Please let me know if you have any questions or concerns about this.
>>
>>     Thanks,
>>     H.
>>
>>     --
>>     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 <mailto:hpages@fhcrc.org>
>>     Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>>     Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>>
>>     ______________________________**___________________
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>> >
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>>
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>> >
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>> >
>>
>>
>>
>
> --
> 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
>
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-- 
*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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