[Bioc-devel] S4 classes extending GRangesList

[Hervé Pagès]

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
>>
>
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>

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
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