[BioC] good news and bad news
hpages at fhcrc.org
Thu Aug 16 19:44:23 CEST 2012
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:
> 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.
> Thanks for the update (where was the bad news?),
> 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 <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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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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