Re: [Bioc-devel] Subsetting an RleList object

Hi Herve, that's brilliant ! Thank you so much for optimizing the method. The new performance is very impressive. Cheers, Thomas [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listin

Re: [Bioc-devel] Subsetting an RleList object

Hi Thomas, In some particular situations seqselect<- was using some tricks to be fast. In IRanges 1.20.6, I've ported these same tricks to [<- so the performance regression you report below should be gone. Let me know if you run into other issues with the subsetting code. Thanks, H. On 11/11/2

Re: [Bioc-devel] Subsetting an RleList object

Saw the fix: could this be considered a bug in the methods package? It seems callNextMethod gets confused with .local(). That said, I like explicit argument passing. On Tue, Oct 29, 2013 at 2:15 PM, Hervé Pagès wrote: > Hi Thomas, > > This is addressed in IRanges 1.20.4 (release) and 1.21.7 (de

Re: [Bioc-devel] Subsetting an RleList object

Hi Herve, thanks a lot for re-enabling the subsetting functionality for CompressedRleList with List-like objects. While things work now, I noticed a big difference in execution time for the following operations: with IRanges_1.18.2 rles <- RleList(Rle(values=TRUE,lengths=1),

Re: [Bioc-devel] Subsetting an RleList object

On 10/30/2013 10:07 AM, Michael Lawrence wrote: On Wed, Oct 30, 2013 at 8:37 AM, Hervé Pagès mailto:hpa...@fhcrc.org>> wrote: On 10/30/2013 07:55 AM, Michael Lawrence wrote: On Tue, Oct 29, 2013 at 5:55 PM, Hervé Pagès mailto:hpa...@fhcrc.org>

Re: [Bioc-devel] Subsetting an RleList object

On Wed, Oct 30, 2013 at 8:37 AM, Hervé Pagès wrote: > > On 10/30/2013 07:55 AM, Michael Lawrence wrote: > >> >> >> >> On Tue, Oct 29, 2013 at 5:55 PM, Hervé Pagès > > wrote: >> >> Hi Michael, >> >> In Bioc < 2.13, subsetting was a mess. In particular, handling of

Re: [Bioc-devel] Subsetting an RleList object

On 10/30/2013 07:55 AM, Michael Lawrence wrote: On Tue, Oct 29, 2013 at 5:55 PM, Hervé Pagès mailto:hpa...@fhcrc.org>> wrote: Hi Michael, In Bioc < 2.13, subsetting was a mess. In particular, handling of list-like subscripts was rather unpredictable. It would work only if yo

Re: [Bioc-devel] Subsetting an RleList object

On Tue, Oct 29, 2013 at 5:55 PM, Hervé Pagès wrote: > Hi Michael, > > In Bioc < 2.13, subsetting was a mess. In particular, handling of > list-like subscripts was rather unpredictable. It would work only > if you were lucky enough to try it with one of the few supported > types (like IntegerList,

Re: [Bioc-devel] Subsetting an RleList object

Hi Michael, In Bioc < 2.13, subsetting was a mess. In particular, handling of list-like subscripts was rather unpredictable. It would work only if you were lucky enough to try it with one of the few supported types (like IntegerList, LogicalList, or IRangesList), but it didn't work for other very

Re: [Bioc-devel] Subsetting an RleList object

I think we should just drop the names for the user. The Bioc <2.13 behavior seems reasonable to me. Please elaborate on the subtle issues. Most users would not expect the *names* on the index to have any effect on the extraction, in accordance with the behavior of ordinary vectors. The only differe

Re: [Bioc-devel] Subsetting an RleList object

Hi Thomas, For the same reasons that you cannot subset by names a Vector object with no names: > IRanges(1:4, width=10)[letters[1:4]] Error in normalizeSingleBracketSubscript(i, x) : cannot subset by character when names are NULL you cannot subset an unnamed List object using a named li

Re: [Bioc-devel] Subsetting an RleList object

Hi Herve, I have updated to IRanges 1.20.4 now, but unfortunately, I still encounter an error when I try to subset a CompressedRleList or SimpleRleList with a CompressedIRangesList or SimpleIRangesList. Would you mind having a look at where I am going wrong ? (My two example objects are available

Re: [Bioc-devel] Subsetting an RleList object

Great ! Thanks a ton for addressing this issue so quickly, Thomas [[alternative HTML version deleted]] ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel

Re: [Bioc-devel] Subsetting an RleList object

Hi Thomas, This is addressed in IRanges 1.20.4 (release) and 1.21.7 (devel). Both should become available thru biocLite() in the next 24 hours or so. Cheers, H. On 10/28/2013 04:01 PM, Hervé Pagès wrote: On 10/28/2013 11:16 AM, Hervé Pagès wrote: Hi Thomas, Thanks for the report. I'm lookin

Re: [Bioc-devel] Subsetting an RleList object

On 10/28/2013 11:16 AM, Hervé Pagès wrote: Hi Thomas, Thanks for the report. I'm looking at this. Will let you know when the problem is fixed. What has changed in BioC 2.13 is that, by default, the RleList() constructor now returns a CompressedRleList object instead of a SimpleRleList object:

Re: [Bioc-devel] Subsetting an RleList object

Hi Thomas, Thanks for the report. I'm looking at this. Will let you know when the problem is fixed. H. On 10/25/2013 11:33 AM, Thomas Sandmann wrote: Sorry, forgot that attachments don't make it through. Here's how to generate the example objects and reproduce the error: library(IRanges) kee

Re: [Bioc-devel] Subsetting an RleList object

Sorry, forgot that attachments don't make it through. Here's how to generate the example objects and reproduce the error: library(IRanges) keep_ranges <- IRangesList( IRanges( start=20, end=108), IRanges( start=41, end=131), IRanges( start=21, end=105)) return_rles <- RleList( Rle(values=TRUE,leng