[Bioc-devel] S4 classes extending GRangesList

[Hervé Pagès]

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