[Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?

Thu Sep 12 08:47:18 CEST 2019

Hi all,

I'm the developer of karyoploteR.

@Michael: I never though about using seqinfo as the source for the 
genome information. I'll add this as an option to define the genome. 
Thanks for the suggestion.

@Aditya: If you want to plot just your relevant chromosomes, you don't 
need to alter the genome. You can use the "chromosomes" parameter to 
give a vector of chromosome names. Is it not working for you for some 
reason?

Bernat

El 9/11/19 a las 2:31 PM, Michael Lawrence via Bioc-devel escribió:
> I'm pretty surprised that the karyoploteR package does not accept a
> Seqinfo since it is plotting chromosomes. But again, please consider
> just doing as(seqinfo(bsgenome), "GRanges").
>
> On Wed, Sep 11, 2019 at 3:59 AM Bhagwat, Aditya
> <Aditya.Bhagwat using mpi-bn.mpg.de> wrote:
>> Hi Herve,
>>
>> Thank you for your responses.
>>  From your response, it is clear that the vcountPDict use case does not need a BSgenome -> GRanges coercer.
>>
>> The karyoploteR use case still requires it, though, to allow plotting of only the chromosomal BSgenome portions:
>>
>>      chromranges <- as(bsegenome, "GRanges")
>>      kp <- karyoploteR::plotKaryotype(chromranges)
>>      karyoploteR::kpPlotRegions(kp, crispr_target_sites)
>>
>> Or do you see any alternative for this purpose too?
>>
>> Aditya
>>
>> ________________________________________
>> From: Pages, Herve [hpages using fredhutch.org]
>> Sent: Wednesday, September 11, 2019 12:24 PM
>> To: Bhagwat, Aditya; bioc-devel using r-project.org
>> Subject: Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?
>>
>> Hi Aditya,
>>
>> On 9/11/19 01:31, Bhagwat, Aditya wrote:
>>> Hi Herve,
>>>
>>>
>>>   > It feels that a coercion method from BSgenome to GRanges should
>>> rather be defined in the BSgenome package itself.
>>>
>>> :-)
>>>
>>>
>>>   > Patch/PR welcome on GitHub.
>>>
>>> Owkies. What pull/fork/check/branch protocol to be followed?
>>>
>>>
>>>   > Is this what you have in mind for this coercion?
>>>   > as(seqinfo(BSgenome.Celegans.UCSC.ce10), "GRanges")
>>>
>>> Yes.
>>>
>>> Perhaps also useful to share the wider context, allowing your and others
>>> feedback for improved software design.
>>> I wanted to subset a
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124367&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=xNa-6ZKTD1MnnfT55tntHjdK51Y1JQGQxTlzX2-OYmI&e=>BSgenome
>>> (without the _random or _unassigned), but Lori explained this is not
>>> possible.
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124367&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=xNa-6ZKTD1MnnfT55tntHjdK51Y1JQGQxTlzX2-OYmI&e=>
>>>
>>> Instead Lori suggested to coerce a BSgenome into a GRanges
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_123489&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=6Eh73QthFfpPsfpRdPWs98pH6GHvv1Z23ORp34OCPxA&e=>,
>>> which is a useful solution, but for which currently no exported S4
>>> method exists
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124416&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=H8owJlOQrNHwNFHfCxGHe27Jxu6xjxpuAMWK8JlTU4Y&e=>
>>> So I defined an S4 coercer in my multicrispr package, making sure to
>>> properly import the Bsgenome class
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124442&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=2XNBVcwoJTjlxY_gl4UPzrHPKmKH9LTnM4ih5SQOfps&e=>.
>>> Then, after coercing a BSgenome into a GRanges, I can extract the
>>> chromosomes, after properly importing IRanges::`%in%`
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124367&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=xNa-6ZKTD1MnnfT55tntHjdK51Y1JQGQxTlzX2-OYmI&e=>
>> Looks like you don't need to coerce the BSgenome object to GRanges. See
>> https://support.bioconductor.org/p/123489/#124581
>>
>> H.
>>
>>> Which I can then on end to karyoploteR
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124328&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=M90_rBO1oohGnXe2XBpQHQriFNthY_W0hzN6KWlf2S4&e=>,
>>> for genome-wide plots of crispr target sites.
>>>
>>> A good moment also to say thank you to all of you who helped me out, it
>>> helps me to make multicrispr fit nicely into the BioC ecosystem.
>>>
>>> Speeking of BioC design philosophy, can any of you suggest concise and
>>> to-the-point reading material to deepen my understanding of the core
>>> BioC software design philosophy?
>>> I am trying to understand that better (which was the context for asking
>>> recently why there are three Vector -> data.frame coercers in S4Vectors
>>> <https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124491&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0aanQY4M6wY&s=nBHdQoTrd1Mfu4VTMgtkPyUQ0Ju2NLeX-0X1Ny3fSeg&e=>)
>>>
>>> Cheers,
>>>
>>> Aditya
>>>
>>>
>>>
>>>
>>> ________________________________________
>>> From: Pages, Herve [hpages using fredhutch.org]
>>> Sent: Tuesday, September 10, 2019 6:45 PM
>>> To: Bhagwat, Aditya; bioc-devel using r-project.org
>>> Subject: Re: [Bioc-devel] Import BSgenome class without attaching
>>> BiocGenerics (and others)?
>>>
>>> Hi Aditya,
>>>
>>>
>>> More generally speaking, coercion methods should be defined in a place
>>> that is "as close as possible" to the "from" or "to" classes rather than
>>> in a package that doesn't own any of the 2 classes involved.
>>> Is this what you have in mind for this coercion?
>>>
>>>   > as(seqinfo(BSgenome.Celegans.UCSC.ce10), "GRanges")
>>> GRanges object with 7 ranges and 0 metadata columns:
>>> seqnames ranges strand
>>> <Rle> <IRanges> <Rle>
>>> chrI chrI 1-15072423 *
>>> chrII chrII 1-15279345 *
>>> chrIII chrIII 1-13783700 *
>>> chrIV chrIV 1-17493793 *
>>> chrV chrV 1-20924149 *
>>> chrX chrX 1-17718866 *
>>> chrM chrM 1-13794 *
>>> -------
>>> seqinfo: 7 sequences (1 circular) from ce10 genome
>>>
>>> Thanks,
>>> H.
>>>
>>>
>>> On 9/6/19 03:39, Bhagwat, Aditya wrote:
>>>   > Dear Bioc devel,
>>>   >
>>>   > Is it possible to import the BSgenome class without attaching
>>> BiocGenerics (to keep a clean namespace during the development of
>>> multicrispr<https://urldefense.proofpoint.com/v2/url?u=https-3A__gitlab.gwdg.de_loosolab_software_multicrispr&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cXJaaEvfNbOioopXgFWQms1qny1xehFQyb3V3xDy55M&s=MIR-kUeXy9oWokdQxItuG82hrvs0uwP1aBIqNdM-Jrs&e=
>>>   >).
>>>   >
>>>   > BSgenome <- methods::getClassDef('BSgenome', package = 'BSgenome')
>>>   >
>>>   > (Posted earlier on BioC
>>> support<https://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_124442_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cXJaaEvfNbOioopXgFWQms1qny1xehFQyb3V3xDy55M&s=oBSScH5uD5j0vCAaj4dfWepjiNGtHm9q5gA8eaIudZ4&e=
>>>   > and redirected here following Martin's suggestion)
>>>   >
>>>   > Thankyou :-)
>>>   >
>>>   > Aditya
>>>   >
>>>   > [[alternative HTML version deleted]]
>>>   >
>>>   > _______________________________________________
>>>   > Bioc-devel using r-project.org mailing list
>>>   >
>>> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=cXJaaEvfNbOioopXgFWQms1qny1xehFQyb3V3xDy55M&s=cEojiObibdSuzmh21opvy85DZyRrjtfo1vEMopKWmAg&e=
>>>   >
>>>
>>> --
>>> 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 using 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 using fredhutch.org
>> Phone:  (206) 667-5791
>> Fax:    (206) 667-1319
>>
>> _______________________________________________
>> Bioc-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
>