[BioC] good news and bad news

[Hervé Pagès]

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...)

   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').

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