[Bioc-devel] as.list of a GRanges
Hi Bernat,
On 02/15/2018 11:57 PM, Bernat Gel wrote:
Hi Herv? and others, Thanks for the responses. I woudn't call as.list() of a GRanges an "obscure behaviour" but more a "works as expected, even if not clearly documented" behaviour.
Most users/developers will probably agree that as.list() worked as expected on a GRanges object. But then they'll be surprised and confused when they use it on an IRanges object and discover that it does something completely different. The current effort is to bring more consistency between GRanges and IRanges objects and to have their list-like semantics aligned and documented so there will be no more such surprise.
In any case I can change the code to as(gr, "GRangesList") as suggested.
I went ahead and fixed karyoploteR. This is karyoploteR 1.5.2. Make sure to resync your GitHub repo by following the instructions here: https://bioconductor.org/developers/how-to/git/sync-existing-repositories/ Note that the loop on the GRanges object (via the call to Map()) was not needed and could be replaced with a solution that uses proper vectorization. Best, H.
Thanks again for the responses and discussion :) Bernat *Bernat Gel Moreno* Bioinformatician Hereditary Cancer Program Program of Predictive and Personalized Medicine of Cancer (PMPPC) Germans Trias i Pujol Research Institute (IGTP) Campus Can Ruti Carretera de Can Ruti, Cam? de les Escoles s/n 08916 Badalona, Barcelona, Spain Tel: (+34) 93 554 3068 Fax: (+34) 93 497 8654 08916 Badalona, Barcelona, Spain bgel at igtp.cat <mailto:bgel at igtp.cat> www.germanstrias.org <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.germanstrias.org_&d=DwMDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Wwl42dL5uGJa8PR0aAcNnIN0t-uut5R2xLKBhl0ynV8&s=z45_PX78N6zLu1Bcn-mYQcyRortvXjNyQcWASriwsr0&e=> <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.germanstrias.org_&d=DwMDaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=Wwl42dL5uGJa8PR0aAcNnIN0t-uut5R2xLKBhl0ynV8&s=z45_PX78N6zLu1Bcn-mYQcyRortvXjNyQcWASriwsr0&e=> El 02/15/2018 a las 11:19 PM, Herv? Pag?s escribi?:
On 02/15/2018 01:57 PM, Michael Lawrence wrote:
On Thu, Feb 15, 2018 at 1:45 PM, Herv? Pag?s <hpages at fredhutch.org <mailto: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.
It's not fair to suggest that this is a widely used feature either. I've identified all the places in the 1500 software packages where this was used, and, as I said, there were very few places. BTW I fixed most of them but my plan is to fix all of them. Some of the code that is outside the Bioc package corpus might be affected but it's fair to assume that this will be a very rare occurence. This can be mitigated by temporary restoring as.list() on GRanges, with a deprecation message, and wait 1 more devel cycle to replace it with the new behavior. I chose to disable it for now, on purpose, so I can identify packages that break (the build report is a great tool for that) and fix them. I'm not using the fact that as.list() on a GRanges is not documented as an excuse for anything. Only to help those with concerns to relativize and relax. H.
???????? ? > 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 ??? -- ??? Herv? Pag?s ??? 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 <mailto:hpages at fredhutch.org> ??? Phone: (206) 667-5791 <tel:%28206%29%20667-5791> ??? Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
Herv? Pag?s 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