[BioC] good news and bad news

Hervé Pagès hpages at fhcrc.org
Thu Aug 16 19:16:13 CEST 2012


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.


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

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