[Bioc-devel] Subsetting an RleList object

[Hervé Pagès]

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)
> keep_ranges <- IRangesList( IRanges( start=20, end=108), IRanges( start=41,
> end=131), IRanges( start=21, end=105))
> return_rles <- RleList( Rle(values=TRUE,lengths=151),
>   Rle(values=TRUE,lengths=151),  Rle(values=TRUE,lengths=151))
> return_rles[ keep_ranges ] <- TRUE
>
> return_rles[ keep_ranges ] ## subsetting works
> return_rles[ keep_ranges ] <- TRUE ## assignment doesn't work
> Error in callNextMethod() :
>    in processing 'callNextMethod', found a '...' in the matched call, but no
> corresponding '...' argument
>
>
>
> On Fri, Oct 25, 2013 at 11:23 AM, Thomas Sandmann <sandmat1 at gene.com> wrote:
>
>> Dear BioC developers,
>>
>> I am trying to subset an RleList with an IRangesList (see attached rdata
>> object). Unfortunately, the following line fails with IRanges 1.20.0:
>>
>> return_rles[keep_ranges] <- TRUE
>> Error in subsetListByList_replace(x, i, value) :
>>    cannot subscript an unnamed list-like object by a named list-like object
>>
>> Unnaming the IRangesList doesn't help, either:
>>
>> return_rles[unname(keep_ranges)] <- TRUE
>> Error in callNextMethod() :
>>    in processing 'callNextMethod', found a '...' in the matched call, but
>> no corresponding '...' argument
>>
>> The same operation worked with IRanges 1.18.2 using the (now deprecated)
>> seqselect method:
>>
>> seqselect( return_rles, keep_ranges ) <- TRUE
>>
>> Any hints ?
>>
>> Thanks,
>> Thomas
>>
>> SessionInfo()
>> R version 3.0.2 (2013-09-25)
>> Platform: x86_64-apple-darwin10.8.0 (64-bit)
>>
>> locale:
>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>>
>> attached base packages:
>> [1] parallel  stats     graphics  grDevices utils     datasets  methods
>> base
>>
>> other attached packages:
>> [1] BiocInstaller_1.12.0 IRanges_1.20.0       BiocGenerics_0.8.0
>> devtools_1.3
>>
>> loaded via a namespace (and not attached):
>> [1] digest_0.6.3   evaluate_0.5.1 httr_0.2       memoise_0.1
>>   RCurl_1.95-4.1 stats4_3.0.2   stringr_0.6.2
>> [8] tools_3.0.2    whisker_0.3-2
>>
>
>
>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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