[Bioc-devel] Import BSgenome class without attaching BiocGenerics (and others)?
Or more accurately: as(seqinfo(bsgenome)[seqlevelsInUse(grl)], "GRanges") since not all seqlevels are necessarily "in use" (i.e. not necessarily represented in seqnames(grl)). H.
On 9/11/19 08:26, Herv? Pag?s wrote:
The unique seqnames is what we call the seqlevels. So just: ? as(seqinfo(bsgenome)[seqlevels(grl)], "GRanges") H. On 9/11/19 07:42, Michael Lawrence wrote:
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 at 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 at gene.com] Sent: Wednesday, September 11, 2019 2:31 PM To: Bhagwat, Aditya Cc: Pages, Herve; bioc-devel at 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 at 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 at fredhutch.org] Sent: Wednesday, September 11, 2019 12:24 PM To: Bhagwat, Aditya; bioc-devel at 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://urldefense.proofpoint.com/v2/url?u=https-3A__support.bioconductor.org_p_123489_-23124581&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ca5pCXdCF2WpOOFAZlUeJVWFkiNt6X-kiDslxFP5AwM&s=kwrPa77YhkAln44Cs7s5Egh_qr247FIVfcEYm52QOcI&e= 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 at fredhutch.org] Sent: Tuesday, September 10, 2019 6:45 PM To: Bhagwat, Aditya; bioc-devel at 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 at 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= ? > -- Herv? Pag?s 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 at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319 -- Herv? Pag?s 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 at fredhutch.org Phone:? (206) 667-5791 Fax:??? (206) 667-1319 _______________________________________________ Bioc-devel at r-project.org mailing list https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwIFaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ca5pCXdCF2WpOOFAZlUeJVWFkiNt6X-kiDslxFP5AwM&s=yjyKVx-pEDq1h66xQ-uTvSa_f74lyyn31nY6cIDRvH4&e= -- Michael Lawrence Scientist, Bioinformatics and Computational Biology Genentech, A Member of the Roche Group Office +1 (650) 225-7760 michafla at gene.com Join Genentech on LinkedIn | Twitter | Facebook | Instagram | YouTube
Herv? Pag?s 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 at fredhutch.org Phone: (206) 667-5791 Fax: (206) 667-1319