Thankyou Bernat, Saw your email just now - since I have the "digest" option. Good that you brought the chromosomes parameter under my attention, I must be able to use that!
Aditya -----Original Message----- From: Bernat Gel Moreno <b...@igtp.cat> Sent: Donnerstag, 12. September 2019 08:47 To: bioc-devel@r-project.org Subject: Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)? 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.bhag...@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 [hpa...@fredhutch.org] >> Sent: Wednesday, September 11, 2019 12:24 PM >> To: Bhagwat, Aditya; bioc-devel@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.biocon >>> ductor.org_p_124367&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvime >>> WdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0a >>> anQY4M6wY&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.biocon >>> ductor.org_p_124367&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvime >>> WdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0a >>> anQY4M6wY&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.biocon >>> ductor.org_p_123489&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvime >>> WdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0a >>> anQY4M6wY&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.biocon >>> ductor.org_p_124416&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvime >>> WdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0a >>> anQY4M6wY&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.biocon >>> ductor.org_p_124367&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvime >>> WdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0a >>> anQY4M6wY&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.biocon >>> ductor.org_p_124328&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvime >>> WdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0a >>> anQY4M6wY&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.biocon >>> ductor.org_p_124491&d=DwMFAw&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvime >>> WdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=FGFwBT0tJu3lfRS_rafeatLzrPxK7PEM0a >>> anQY4M6wY&s=nBHdQoTrd1Mfu4VTMgtkPyUQ0Ju2NLeX-0X1Ny3fSeg&e=>) >>> >>> Cheers, >>> >>> Aditya >>> >>> >>> >>> >>> ________________________________________ >>> From: Pages, Herve [hpa...@fredhutch.org] >>> Sent: Tuesday, September 10, 2019 6:45 PM >>> To: Bhagwat, Aditya; bioc-devel@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@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: hpa...@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: hpa...@fredhutch.org >> Phone: (206) 667-5791 >> Fax: (206) 667-1319 >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel > > _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
