[BioC] good news and bad news
Kasper Daniel Hansen
kasperdanielhansen at gmail.com
Thu Aug 16 22:14:39 CEST 2012
Thanks Herve, this change is much appreciated.
On Thu, Aug 16, 2012 at 2:02 PM, Tim Triche, Jr. <tim.triche at gmail.com> wrote:
> Right around the time I get used to using values(GR) all over the place...
> and, an excellent opportunity to improve R's Unicode support, squandered!
> As long as things work right for SummarizedExperiments and their coercions
> to/from other common data structures, I'm certainly not going to complain.
> I'm not sure how I feel about having urged Hervé and Martin to compromise
> their principles about this, but it will make some peoples' lives a lot
> Not least, mine, as I try to get examples and documentation completed for
> the 'regulatoR' package I've been working on lately.
> Having seen the logic behind your original design decisions, I understand
> why you were reluctant to do this.
> If it turns out that we have demanded "enough rope to shoot ourself in the
> foot", well, we asked for it!
> So, thank you, quite a lot, for including something that could well be as
> dangerous as it is handy.
> On Thu, Aug 16, 2012 at 10:44 AM, Hervé Pagès <hpages at fhcrc.org> wrote:
>> 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:
>>> 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
>>> (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>
>>> Bioconductor mailing list
>>> Bioconductor at r-project.org <mailto:Bioconductor at r-**project.org<Bioconductor at r-project.org>
>>> Search the archives:
>> 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
>> Bioconductor mailing list
>> Bioconductor at r-project.org
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