[Bioc-devel] S4 classes extending GRangesList

[Leonard Goldstein]

Thanks Hervé.

Best wishes,

Leonard


On Thu, Jun 11, 2015 at 10:58 AM, Hervé Pagès <hpages at fredhutch.org> wrote:
> Hi Leonard,
>
> It's a bug in the "c" method for "CompressedList" object. I'll fix
> that. Thanks for the report.
>
> H.
>
>
> On 06/11/2015 10:48 AM, Leonard Goldstein wrote:
>>
>> Hi all,
>>
>> I noticed that when combining instances of a class that inherits from
>> GRangesList, the result does not preserve the class (it is returned as
>> a GRangesList instead). The class is preserved in other situations
>> (e.g. when a class extends GRanges). See below for an example. Is
>> there a reason why the class cannot be preserved in the first case?
>> Thanks in advance for your help.
>>
>> Leonard
>>
>>
>>> ## define a new class 'A' inheriting from GRanges
>>> setClass(Class = "A", contains = "GRanges")
>>>
>>> ## combining two instances of class 'A' returns an object of class 'A'
>>> gr <- GRanges("1", IRanges(1, 100))
>>> a <- new("A", gr)
>>> a
>>
>> A object with 1 range and 0 metadata columns:
>>        seqnames    ranges strand
>>           <Rle> <IRanges>  <Rle>
>>    [1]        1  [1, 100]      *
>>    -------
>>    seqinfo: 1 sequence from an unspecified genome; no seqlengths
>>>
>>> c(a, a)
>>
>> A object with 2 ranges and 0 metadata columns:
>>        seqnames    ranges strand
>>           <Rle> <IRanges>  <Rle>
>>    [1]        1  [1, 100]      *
>>    [2]        1  [1, 100]      *
>>    -------
>>    seqinfo: 1 sequence from an unspecified genome; no seqlengths
>>>
>>>
>>> ## define a new class 'b' inheriting from GRangesList
>>> setClass(Class = "B", contains = "GRangesList")
>>>
>>> ## combining two instances of class 'B' returns a GRangesList
>>> grl <- split(gr, 1)
>>> b <- new("B", grl)
>>> b
>>
>> B object of length 1:
>> $1
>> GRanges object with 1 range and 0 metadata columns:
>>        seqnames    ranges strand
>>           <Rle> <IRanges>  <Rle>
>>    [1]        1  [1, 100]      *
>>
>> -------
>> seqinfo: 1 sequence from an unspecified genome; no seqlengths
>>>
>>> c(b, b)
>>
>> GRangesList object of length 2:
>> $1
>> GRanges object with 1 range and 0 metadata columns:
>>        seqnames    ranges strand
>>           <Rle> <IRanges>  <Rle>
>>    [1]        1  [1, 100]      *
>>
>> $1
>> GRanges object with 1 range and 0 metadata columns:
>>        seqnames   ranges strand
>>    [1]        1 [1, 100]      *
>>
>> -------
>> seqinfo: 1 sequence from an unspecified genome; no seqlengths
>>>
>>>
>>> sessionInfo()
>>
>> R Under development (unstable) (2014-11-04 r66932)
>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>
>> locale:
>>   [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
>>   [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
>>   [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
>>   [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
>>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats4    parallel  stats     graphics  grDevices utils     datasets
>> [8] methods   base
>>
>> other attached packages:
>> [1] GenomicRanges_1.21.15 GenomeInfoDb_1.5.7    IRanges_2.3.11
>> [4] S4Vectors_0.7.4       BiocGenerics_0.15.2
>>
>> loaded via a namespace (and not attached):
>> [1] XVector_0.9.1
>>>
>>>
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>
> --
> 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 at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319