[Bioc-devel] Subsetting an RleList object

[Hervé Pagès]

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 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:
>
>    return_rles <- RleList(Rle(values=TRUE,lengths=151),
>                           Rle(values=TRUE,lengths=151),
>                           Rle(values=TRUE,lengths=151))
> Then:
>
>    > class(return_rles)      # used to be SimpleRleList (in BioC < 2.13)
>    [1] "CompressedRleList"
>    attr(,"package")
>    [1] "IRanges"
>
> and `[<-` doesn't work (and never has) on a CompressedRleList object
> when the subscript is a list-like object:
>
>    > return_rles[ list(20:108, 41:131, 21:105) ] <- TRUE
>    Error in callNextMethod() :
>      in processing 'callNextMethod', found a '...' in the matched call,
>      but no corresponding '...' argument
>
> So an immeadiate work-around for you is to call RleList() with
> 'compress=FALSE' to create a SimpleRleList object:
>
>    return_rles <- RleList(Rle(values=TRUE,lengths=151),
>                           Rle(values=TRUE,lengths=151),
>                           Rle(values=TRUE,lengths=151),
>                           compress=FALSE)
>
> Then:
>
>    > return_rles[ list(20:108, 41:131, 21:105) ] <- TRUE
>
> This also works with an IRangesList subscript:
>
>    keep_ranges <- IRangesList(IRanges(start=20, end=108),
>                               IRanges(start=41, end=131),
>                               IRanges(start=21, end=105))
>
> Then:
>
>    > return_rles[ keep_ranges ] <- TRUE
>
> 2 issues that need to be addressed:
>    (1) `[<-` should work on a CompressedRleList object when using a
>        list-like subscript.
>    (2) The RleList() constructor should warn that its behavior has
>        changed when called without specifying the 'compress' arg.
> A fix is on its way.
>
> H.
>
>
>>
>> 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
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