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
