[Bioc-devel] as.list of a GRanges

Cook, Malcolm MEC at stowers.org
Thu Feb 15 20:53:23 CET 2018


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...

 > 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?



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