[Bioc-devel] S4 classes extending GRangesList

[Leonard Goldstein]

Great, thank you Hervé.

Best wishes,

Leonard

On Tue, Sep 29, 2015 at 2:07 PM, Hervé Pagès <hpages at fredhutch.org> wrote:
> Hi Leonard,
>
> Fixed in IRanges 2.3.22 (devel) and 2.2.8 (release). Now the "c" method
> for CompressedList objects should always return an object of the same
> class as its 1st argument.
>
> Thanks for your patience and for the reminder.
> H.
>
>
> On 09/29/2015 10:35 AM, Leonard Goldstein wrote:
>>
>> Hi Hervé,
>>
>> This still looks broken in the current bioc-devel. Just wanted to
>> follow up in case it got missed. Thanks again.
>>
>> Leonard
>>
>>
>>
>> On Thu, Jun 11, 2015 at 11:59 AM, Leonard Goldstein <goldstel at gene.com>
>> wrote:
>>>
>>> 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
>
>
> --
> 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