[BioC] good news and bad news

[Hervé Pagès]

Hi Michael,

On 08/16/2012 10:25 AM, Michael Lawrence wrote:
>
>
> On Thu, Aug 16, 2012 at 10:16 AM, Hervé Pagès <hpages at fhcrc.org
> <mailto:hpages at 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 at fhcrc.org <mailto:hpages at fhcrc.org>
>     Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>     Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>
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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 at fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319