I've hit this many times and would appreciate support for NA indices.

Michael


On Mon, Mar 10, 2014 at 1:12 PM, Hervé Pagès <hpages@fhcrc.org> wrote:

> Hi Malcolm,
>
> On one hand, Rle is a Vector subclass and subsetting an Rle is
> consistent with subsetting any other Vector subclass (like IRanges,
> GRanges, DNAStringSet, etc...) where trying to extract an element
> that doesn't exist raises an error. Of course, this is the only
> choice for those Vector derivative (that are not Rle's) because
> they don't support NAs.
>
> On the other hand, Rle is a memory efficient replacement for ordinary
> atomic vectors, and, ideally, they should be substitutable (which
> means the former should mimic the latter as close as possible).
>
> A choice had to be made 5 years ago when Rle's were implemented
> in the IRanges package. Should we revisit that choice and support
> subsetting of an Rle by an out-of-bound subscript? Should we also
> support NAs in the subscript?
>
> Thanks,
> H.
>
>
>
> On 03/10/2014 11:52 AM, Cook, Malcolm wrote:
>
>> I think the semantics of indexing into an Rles should be the same as
>> indexing into the corresponding vector.
>>
>> But it is not in the case when indices are out of bounds.
>>
>> Example:
>>
>> library(IRanges)
>>
>>> c(1:10)[10:13]
>>>
>> [1] 10 NA NA NA
>>
>>  Rle(c(1:10))[10:13]
>>>
>> Error in normalizeSingleBracketSubscript(i, x) :
>>    subscript contains NAs or out of bounds indices
>>
>>
>> I've made similar arguments before which were taken up, as in
>> https://stat.ethz.ch/pipermail/bioconductor/2013-September/054820.html
>>
>> Is there a good reason NOT to change these semantics?
>>
>> In the meantime, any suggested clever workarounds to get such extraction
>> semantics?
>>
>> Thanks!
>>
>> ~ Malcolm Cook
>> Computational Biology / Shilatifard Lab - Stowers Institute for Medical
>> Research - Kansas City
>>
>>
>>
> --
> Hervé Pagès
>
> 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@fhcrc.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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