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.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 [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 -- Michael Lawrence Scientist, Bioinformatics and Computational Biology Genentech, A Member of the Roche Group Office +1 (650) 225-7760 micha...@gene.com Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
