[Bioc-devel] as.list of a GRanges

Michael Lawrence lawrence.michael at gene.com
Thu Feb 15 21:00:36 CET 2018

On Thu, Feb 15, 2018 at 11:53 AM, Cook, Malcolm <MEC at stowers.org> wrote:

> Hi,
> Can I ask, is this change under discussion in current release or so far in
> Bioconductor devel only (my assumption)?
>  > 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...
Yes, this is what I meant. The Bioc package corpus is not very
representative for some of these entry points. Please keep that in mind
when making refactoring decisions.

>  > 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.
Please be careful with these changes in behavior. Given the amount of code
that now depends on this software, consistency with existing behavior needs
to be weighted heavily.

> Can we please be assured to be reminded of this prominently in release
> notes?
> Thanks!
> ~malcolm

	[[alternative HTML version deleted]]

More information about the Bioc-devel mailing list