On Thu, Aug 16, 2012 at 10:16 AM, Hervé Pagès <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.



>   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.

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
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
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