[Bioc-devel] as.list of a GRanges

Hervé Pagès hpages at fredhutch.org
Thu Feb 15 22:45:53 CET 2018

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.

>   > 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.


> Thanks!
> ~malcolm

Hervé Pagès

Program in Computational Biology
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