[Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?
Michael Lawrence
|@wrence@m|ch@e| @end|ng |rom gene@com
Wed Sep 11 16:42:34 CEST 2019
So why not just do:
as(seqinfo(bsgenome)[unique(unlist(seqnames(grl)))], "GRanges")
Michael
On Wed, Sep 11, 2019 at 5:55 AM Bhagwat, Aditya
<Aditya.Bhagwat using mpi-bn.mpg.de> wrote:
>
> Thanks Michael,
>
> The important detail is that I want to plot the relevant chromosomes only
>
> relevant_chromosomes <- GenomeInfoDb::seqnames(grangeslist) %>%
> S4Vectors::runValue() %>%
> Reduce(union, .) %>%
> unique()
>
> genomeranges <- GenomeInfoDb::seqinfo(grangeslist) %>%
> as('GRanges') %>%
> (function(gr){
> gr [ as.character(GenomeInfoDb::seqnames(gr)) %in%
> relevant_chromosomes ]
> })
>
> kp <- karyoploteR::plotKaryotype(genomeranges)
> karyoploteR::kpPlotRegions(kp, grangeslist) # grangeslist contains crispr target sites
>
>
> And, this process required as("GRanges")
>
> #' Convert BSgenome into GRanges
> #' @param from BSgenome, e.g. BSgenome.Mmusculus.UCSC.mm10::Mmusculus
> #' @examples
> #' require(magrittr)
> #' BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10 %>%
> #' as('GRanges')
> #' @importClassesFrom BSgenome BSgenome
> #' @export
> methods::setAs( "BSgenome",
> "GRanges",
> function(from) from %>%
> GenomeInfoDb::seqinfo() %>%
> as('GRanges'))
>
> Thankyou for feedback,
>
> Aditya
>
> ________________________________________
> From: Michael Lawrence [lawrence.michael using gene.com]
> Sent: Wednesday, September 11, 2019 2:31 PM
> To: Bhagwat, Aditya
> Cc: Pages, Herve; bioc-devel using r-project.org
> Subject: Re: [Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?
>
> 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
>
>
>
> --
> Michael Lawrence
> Scientist, Bioinformatics and Computational Biology
> Genentech, A Member of the Roche Group
> Office +1 (650) 225-7760
> michafla using gene.com
>
> Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube
--
Michael Lawrence
Scientist, Bioinformatics and Computational Biology
Genentech, A Member of the Roche Group
Office +1 (650) 225-7760
michafla using gene.com
Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube
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