[Bioc-devel] as.list of a GRanges

[Michael Lawrence]

On Thu, Feb 15, 2018 at 1:45 PM, Hervé Pagès <hpages at fredhutch.org> wrote:

> On 02/15/2018 11:53 AM, Cook, Malcolm wrote:
>
>> Hi,
>>
>> Can I ask, is this change under discussion in current release or so far
>> in Bioconductor devel only (my assumption)?
>>
>
> Bioconductor devel only.
>
>
>>   > On 02/15/2018 08:37 AM, Michael Lawrence wrote:
>>   > > So is as.list() no longer supported for GRanges objects? I have
>> found it
>>   > > useful in places.
>>   >
>>   > Very few places. I found a dozen of them in the entire software repo.
>>
>> However there are probably more in the wild...
>>
>
> What as.list() was doing on a GRanges object was not documented. Relying
> on some kind of obscure undocumented feature is never a good idea.
>
>
There's just too much that is documented implicitly through inherited
behaviors, or where we say things like "this data structure behaves as one
would expect given base R". It's not fair to claim that those features are
undocumented. Our documentation is not complete enough to use it as an
excuse.


>
>>   > Now you should use as.list(as(gr, "GRangesList")) instead.
>>   > as.list() was behaving inconsistently on IRanges and GRanges objects,
>>   > which is blocking new developments. It will come back with a
>> consistent
>>   > behavior. More generally speaking IRanges and GRanges will behave
>>   > consistently as far as their "list interpretation" is concerned.
>>
>> Can we please be assured to be reminded of this prominently in release
>> notes?
>>
>
> The changes will be announced and described on this list and in the
> NEWS files of the IRanges and GenomicRanges packages.
>
> H.
>
>
>> Thanks!
>>
>> ~malcolm
>>
>>
> --
> 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 fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>
>

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