In WGBS we frequently sequence a human with spikein from the lambda
genome. In this case, most of the chromosomes of the Granges are from
human, except one. This is a usecase where genome(GR) is not constant. I
suggest, partly for compatibility, to keep genome, but perhaps do something
like
standardizeGenome()
or something like this.
I would indeed love, love, love a function which just cleans it up.
Kasper
On Fri, Jun 5, 2015 at 2:51 PM, Gabe Becker <becker.g...@gene.com> wrote:
> Herve,
>
> This is probably a naive question, but what usecases are there for creating
> an object with the wrong seqinfo for its genome?
>
> ~G
>
> On Fri, Jun 5, 2015 at 11:43 AM, Michael Lawrence <
> lawrence.mich...@gene.com
> > wrote:
>
> > On Thu, Jun 4, 2015 at 11:48 PM, Hervé Pagès <hpa...@fredhutch.org>
> wrote:
> > > I also think that we're heading towards something like that.
> > >
> > > So genome(gr) <- "hg19" would:
> > >
> > > (a) Add any missing information to the seqinfo.
> > > (b) Sort the seqlevels in "canonical" order.
> > > (c) Change the seqlevels style to UCSC style if they are not.
> > >
> > > The 3 tasks are orthogonal. I guess most of the times people want
> > > an easy way to perform them all at once.
> > >
> > > We could easily support (a) and (b). This assumes that the current
> > > seqlevels are already valid hg19 seqlevels:
> > >
> > > si1 <- Seqinfo(c("chrX", "chrUn_gl000249", "chr2", "chr6_cox_hap2"))
> > > gr1 <- GRanges(seqinfo=si1)
> > > hg19_si <- Seqinfo(genome="hg19")
> > >
> > > ## (a):
> > > seqinfo(gr1) <- merge(seqinfo(gr1), hg19_si)[seqlevels(gr1)]
> > > seqinfo(gr1)
> > > # Seqinfo object with 4 sequences (1 circular) from hg19 genome:
> > > # seqnames seqlengths isCircular genome
> > > # chrX 155270560 FALSE hg19
> > > # chrUn_gl000249 38502 FALSE hg19
> > > # chr2 243199373 FALSE hg19
> > > # chr6_cox_hap2 4795371 FALSE hg19
> > >
> > > ## (b):
> > > seqlevels(gr1) <- intersect(seqlevels(hg19_si), seqlevels(gr1))
> > > seqinfo(gr1)
> > > # Seqinfo object with 4 sequences (1 circular) from hg19 genome:
> > > # seqnames seqlengths isCircular genome
> > > # chr2 243199373 FALSE hg19
> > > # chrX 155270560 FALSE hg19
> > > # chr6_cox_hap2 4795371 FALSE hg19
> > > # chrUn_gl000249 38502 FALSE hg19
> > >
> > > (c) is harder because seqlevelsStyle() doesn't know how to rename
> > > scaffolds yet:
> > >
> > > si2 <- Seqinfo(c("X", "HSCHRUN_RANDOM_CTG42", "2",
> > "HSCHR6_MHC_COX_CTG1"))
> > > gr2 <- GRanges(seqinfo=si2)
> > >
> > > seqlevelsStyle(gr2)
> > > # [1] "NCBI"
> > >
> > > seqlevelsStyle(gr2) <- "UCSC"
> > > seqlevels(gr2)
> > > # [1] "chrX" "HSCHRUN_RANDOM_CTG42" "chr2"
> > > # [4] "HSCHR6_MHC_COX_CTG1"
> > >
> > > So we need to work on this.
> > >
> > > I'm not sure about using genome(gr) <- "hg19" for this. Right now
> > > it sets the genome column of the seqinfo with the supplied string
> > > and nothing else. Aren't there valid use cases for this?
> >
> > Not sure. People would almost always want the seqname style and order
> > to be consistent with the given genome.
> >
> > > What about
> > > using seqinfo(gr) <- "hg19" instead? It kind of suggests that the
> > > whole seqinfo component actually gets filled.
> > >
> >
> > Yea, but "genome" is so intuitive compared to "seqinfo".
> >
> >
> >
> > > H.
> > >
> > > On 06/04/2015 06:30 PM, Tim Triche, Jr. wrote:
> > >>
> > >> that's kind of always been my goal...
> > >>
> > >>
> > >> Statistics is the grammar of science.
> > >> Karl Pearson <http://en.wikipedia.org/wiki/The_Grammar_of_Science>
> > >>
> > >> On Thu, Jun 4, 2015 at 6:29 PM, Michael Lawrence
> > >> <lawrence.mich...@gene.com <mailto:lawrence.mich...@gene.com>> wrote:
> > >>
> > >> Maybe this could eventually support setting the seqinfo with:
> > >>
> > >> genome(gr) <- "hg19"
> > >>
> > >> Or is that being too clever?
> > >>
> > >> On Thu, Jun 4, 2015 at 4:28 PM, Hervé Pagès <hpa...@fredhutch.org
> > >> <mailto:hpa...@fredhutch.org>> wrote:
> > >> > Hi,
> > >> >
> > >> > FWIW I started to work on supporting quick generation of a
> > >> standalone
> > >> > Seqinfo object via Seqinfo(genome="hg38") in GenomeInfoDb.
> > >> >
> > >> > It already supports hg38, hg19, hg18, panTro4, panTro3,
> panTro2,
> > >> > bosTau8, bosTau7, bosTau6, canFam3, canFam2, canFam1, musFur1,
> > >> mm10,
> > >> > mm9, mm8, susScr3, susScr2, rn6, rheMac3, rheMac2, galGal4,
> > >> galGal3,
> > >> > gasAcu1, danRer7, apiMel2, dm6, dm3, ce10, ce6, ce4, ce2,
> > sacCer3,
> > >> > and sacCer2. I'll add more.
> > >> >
> > >> > See ?Seqinfo for some examples.
> > >> >
> > >> > Right now it fetches the information from internet every time
> you
> > >> > call it but maybe we should just store that information in the
> > >> > GenomeInfoDb package as Tim suggested?
> > >> >
> > >> > H.
> > >> >
> > >> >
> > >> > On 06/03/2015 12:54 PM, Tim Triche, Jr. wrote:
> > >> >>
> > >> >> That would be perfect actually. And it would radically
> reduce &
> > >> >> modularize maintenance. Maybe that's the best way to go after
> > >> all. Quite
> > >> >> sensible.
> > >> >>
> > >> >> --t
> > >> >>
> > >> >>> On Jun 3, 2015, at 12:46 PM, Vincent Carey
> > >> <st...@channing.harvard.edu <mailto:st...@channing.harvard.edu>>
> > >> >>> wrote:
> > >> >>>
> > >> >>> It really isn't hard to have multiple OrganismDb packages in
> > >> place -- the
> > >> >>> process of making new ones is documented and was given as an
> > >> exercise in
> > >> >>> the EdX course. I don't know if we want to institutionalize
> it
> > >> and
> > >> >>> distribute such -- I think we might, so that there would be
> > >> Hs19, Hs38,
> > >> >>> mm9, etc. packages. They have very little content, they just
> > >> coordinate
> > >> >>> interactions with packages that you'll already have.
> > >> >>>
> > >> >>> On Wed, Jun 3, 2015 at 3:26 PM, Tim Triche, Jr.
> > >> <tim.tri...@gmail.com <mailto:tim.tri...@gmail.com>>
> > >>
> > >> >>> wrote:
> > >> >>>
> > >> >>>> Right, I typically do that too, and if you're working on
> human
> > >> data it
> > >> >>>> isn't a big deal. What makes things a lot more of a drag is
> > >> when you
> > >> >>>> work
> > >> >>>> on e.g. mouse data (mm9 vs mm10, aka GRCm37 vs GRCm38) where
> > >> >>>> Mus.musculus
> > >> >>>> is essentially a "build ahead" of Homo.sapiens.
> > >> >>>>
> > >> >>>> R> seqinfo(Homo.sapiens)
> > >> >>>> Seqinfo object with 93 sequences (1 circular) from hg19
> genome
> > >> >>>>
> > >> >>>> R> seqinfo(Mus.musculus)
> > >> >>>> Seqinfo object with 66 sequences (1 circular) from mm10
> > genome:
> > >> >>>>
> > >> >>>> It's not as explicit as directly assigning the seqinfo from
> a
> > >> genome
> > >> >>>> that
> > >> >>>> corresponds to that of your annotations/results/whatever. I
> > >> know we
> > >> >>>> could
> > >> >>>> all use crossmap or liftOver or whatever, but that's not
> > >> really the
> > >> >>>> same,
> > >> >>>> and it takes time, whereas assigning the proper seqinfo for
> > >> >>>> relationships
> > >> >>>> is very fast.
> > >> >>>>
> > >> >>>> That's all I was getting at...
> > >> >>>>
> > >> >>>>
> > >> >>>> Statistics is the grammar of science.
> > >> >>>> Karl Pearson
> > >> <http://en.wikipedia.org/wiki/The_Grammar_of_Science>
> > >> >>>>
> > >> >>>> On Wed, Jun 3, 2015 at 12:17 PM, Vincent Carey
> > >> >>>> <st...@channing.harvard.edu <mailto:
> > st...@channing.harvard.edu>
> > >> >>>>>
> > >> >>>>> wrote:
> > >> >>>>
> > >> >>>>
> > >> >>>>> I typically get this info from Homo.sapiens. The result is
> > >> parasitic
> > >> >>>>> on
> > >> >>>>> the TxDb that is in there. I don't know how easy it is to
> > swap
> > >> >>>>> alternate
> > >> >>>>> TxDb in to get a different build. I think it would make
> > sense
> > >> to
> > >> >>>>> regard
> > >> >>>>> the OrganismDb instances as foundational for this sort of
> > >> structural
> > >> >>>>> data.
> > >> >>>>>
> > >> >>>>> On Wed, Jun 3, 2015 at 3:12 PM, Kasper Daniel Hansen <
> > >> >>>>> kasperdanielhan...@gmail.com
> > >> <mailto:kasperdanielhan...@gmail.com>> wrote:
> > >> >>>>>
> > >> >>>>>> Let me rephrase this slightly. From one POV the purpose
> of
> > >> >>>>>> GenomeInfoDb
> > >> >>>>>> is
> > >> >>>>>> clean up the seqinfo slot. Currently it does most of the
> > >> cleaning,
> > >> >>>>>> but
> > >> >>>>>> it
> > >> >>>>>> does not add seqlengths.
> > >> >>>>>>
> > >> >>>>>> It is clear that seqlengths depends on the version of the
> > >> genome, but
> > >> >>>>>> I
> > >> >>>>>> will argue so does the seqnames. Of course, for human,
> > >> chr22 will not
> > >> >>>>>> change. But what about the names of all the random
> > >> contigs? Or for
> > >> >>>>>> other
> > >> >>>>>> organisms, what about going from a draft genome with 10k
> > >> contigs to a
> > >> >>>>>> more
> > >> >>>>>> completely genome assembled into fewer, larger
> chromosomes.
> > >> >>>>>>
> > >> >>>>>> I acknowledge that this information is present in the
> > BSgenome
> > >> >>>>>> packages,
> > >> >>>>>> but it seems (to me) to be very appropriate to have them
> > >> around for
> > >> >>>>>> cleaning up the seqinfo slot. For some situations it is
> not
> > >> great to
> > >> >>>>>> depend on 1 GB> download for something that is a few
> bytes.
> > >> >>>>>>
> > >> >>>>>> Best,
> > >> >>>>>> Kasper
> > >> >>>>>>
> > >> >>>>>> On Wed, Jun 3, 2015 at 3:00 PM, Tim Triche, Jr.
> > >> <tim.tri...@gmail.com <mailto:tim.tri...@gmail.com>>
> > >>
> > >> >>>>>> wrote:
> > >> >>>>>>
> > >> >>>>>>> It would be nice (for a number of reasons) to have
> > >> chromosome lengths
> > >> >>>>>>> readily available in a foundational package like
> > >> GenomeInfoDb, so
> > >> >>>>>>> that,
> > >> >>>>>>> say,
> > >> >>>>>>>
> > >> >>>>>>> data(seqinfo.hg19)
> > >> >>>>>>> seqinfo(myResults) <- seqinfo.hg19[ seqlevels(myResults)
> ]
> > >> >>>>>>>
> > >> >>>>>>> would work without issues. Is there any particular
> reason
> > >> this
> > >> >>>>>>
> > >> >>>>>> couldn't
> > >> >>>>>>>
> > >> >>>>>>> happen for the supported/available BSgenomes? It would
> > >> seem like a
> > >> >>>>>>
> > >> >>>>>> simple
> > >> >>>>>>>
> > >> >>>>>>> matter to do
> > >> >>>>>>>
> > >> >>>>>>> R> library(BSgenome.Hsapiens.UCSC.hg19)
> > >> >>>>>>> R> seqinfo.hg19 <- seqinfo(Hsapiens)
> > >> >>>>>>> R> save(seqinfo.hg19,
> > >> >>>>>>> file="~/bioc-devel/GenomeInfoDb/data/seqinfo.hg19.rda")
> > >> >>>>>>>
> > >> >>>>>>> and be done with it until (say) the next release or next
> > >> released
> > >> >>>>>>> BSgenome. I considered looping through the following
> > >> BSgenomes
> > >> >>>>>>
> > >> >>>>>> myself...
> > >> >>>>>>>
> > >> >>>>>>> and if it isn't strongly opposed by (everyone) I may
> still
> > >> do exactly
> > >> >>>>>>> that. Seems useful, no?
> > >> >>>>>>>
> > >> >>>>>>> e.g. for the following 42 builds,
> > >> >>>>>>>
> > >> >>>>>>> grep("(UCSC|NCBI)", unique(gsub(".masked", "",
> > >> available.genomes())),
> > >> >>>>>>> value=TRUE)
> > >> >>>>>>> [1] "BSgenome.Amellifera.UCSC.apiMel2"
> > >> >>>>>>
> > >> >>>>>> "BSgenome.Btaurus.UCSC.bosTau3"
> > >> >>>>>>>
> > >> >>>>>>>
> > >> >>>>>>> [3] "BSgenome.Btaurus.UCSC.bosTau4"
> > >> >>>>>>
> > >> >>>>>> "BSgenome.Btaurus.UCSC.bosTau6"
> > >> >>>>>>>
> > >> >>>>>>>
> > >> >>>>>>> [5] "BSgenome.Btaurus.UCSC.bosTau8"
> > >> >>>>>>> "BSgenome.Celegans.UCSC.ce10"
> > >> >>>>>>>
> > >> >>>>>>> [7] "BSgenome.Celegans.UCSC.ce2"
> > >> "BSgenome.Celegans.UCSC.ce6"
> > >> >>>>>>>
> > >> >>>>>>> [9] "BSgenome.Cfamiliaris.UCSC.canFam2"
> > >> >>>>>>> "BSgenome.Cfamiliaris.UCSC.canFam3"
> > >> >>>>>>> [11] "BSgenome.Dmelanogaster.UCSC.dm2"
> > >> >>>>>>> "BSgenome.Dmelanogaster.UCSC.dm3"
> > >> >>>>>>> [13] "BSgenome.Dmelanogaster.UCSC.dm6"
> > >> >>>>>>
> > >> >>>>>> "BSgenome.Drerio.UCSC.danRer5"
> > >> >>>>>>>
> > >> >>>>>>>
> > >> >>>>>>> [15] "BSgenome.Drerio.UCSC.danRer6"
> > >> >>>>>>
> > >> >>>>>> "BSgenome.Drerio.UCSC.danRer7"
> > >> >>>>>>>
> > >> >>>>>>>
> > >> >>>>>>> [17] "BSgenome.Ecoli.NCBI.20080805"
> > >> >>>>>>> "BSgenome.Gaculeatus.UCSC.gasAcu1"
> > >> >>>>>>> [19] "BSgenome.Ggallus.UCSC.galGal3"
> > >> >>>>>>
> > >> >>>>>> "BSgenome.Ggallus.UCSC.galGal4"
> > >> >>>>>>>
> > >> >>>>>>>
> > >> >>>>>>> [21] "BSgenome.Hsapiens.NCBI.GRCh38"
> > >> >>>>>>> "BSgenome.Hsapiens.UCSC.hg17"
> > >> >>>>>>>
> > >> >>>>>>> [23] "BSgenome.Hsapiens.UCSC.hg18"
> > >> >>>>>>> "BSgenome.Hsapiens.UCSC.hg19"
> > >> >>>>>>>
> > >> >>>>>>> [25] "BSgenome.Hsapiens.UCSC.hg38"
> > >> >>>>>>> "BSgenome.Mfascicularis.NCBI.5.0"
> > >> >>>>>>> [27] "BSgenome.Mfuro.UCSC.musFur1"
> > >> >>>>>>
> > >> >>>>>> "BSgenome.Mmulatta.UCSC.rheMac2"
> > >> >>>>>>>
> > >> >>>>>>>
> > >> >>>>>>> [29] "BSgenome.Mmulatta.UCSC.rheMac3"
> > >> >>>>>>
> > >> >>>>>> "BSgenome.Mmusculus.UCSC.mm10"
> > >> >>>>>>>
> > >> >>>>>>>
> > >> >>>>>>> [31] "BSgenome.Mmusculus.UCSC.mm8"
> > >> >>>>>>> "BSgenome.Mmusculus.UCSC.mm9"
> > >> >>>>>>>
> > >> >>>>>>> [33] "BSgenome.Ptroglodytes.UCSC.panTro2"
> > >> >>>>>>> "BSgenome.Ptroglodytes.UCSC.panTro3"
> > >> >>>>>>> [35] "BSgenome.Rnorvegicus.UCSC.rn4"
> > >> >>>>>>
> > >> >>>>>> "BSgenome.Rnorvegicus.UCSC.rn5"
> > >> >>>>>>>
> > >> >>>>>>>
> > >> >>>>>>> [37] "BSgenome.Rnorvegicus.UCSC.rn6"
> > >> >>>>>>> "BSgenome.Scerevisiae.UCSC.sacCer1"
> > >> >>>>>>> [39] "BSgenome.Scerevisiae.UCSC.sacCer2"
> > >> >>>>>>> "BSgenome.Scerevisiae.UCSC.sacCer3"
> > >> >>>>>>> [41] "BSgenome.Sscrofa.UCSC.susScr3"
> > >> >>>>>>
> > >> >>>>>> "BSgenome.Tguttata.UCSC.taeGut1"
> > >> >>>>>>>
> > >> >>>>>>>
> > >> >>>>>>>
> > >> >>>>>>>
> > >> >>>>>>>
> > >> >>>>>>> Am I insane for suggesting this? It would make things a
> > >> little
> > >> >>>>>>> easier
> > >> >>>>>>
> > >> >>>>>> for
> > >> >>>>>>>
> > >> >>>>>>> rtracklayer, most SummarizedExperiment and SE-derived
> > >> objects, blah,
> > >> >>>>>>
> > >> >>>>>> blah,
> > >> >>>>>>>
> > >> >>>>>>> blah...
> > >> >>>>>>>
> > >> >>>>>>>
> > >> >>>>>>> Best,
> > >> >>>>>>>
> > >> >>>>>>> --t
> > >> >>>>>>>
> > >> >>>>>>>
> > >> >>>>>>>
> > >> >>>>>>>
> > >> >>>>>>> Statistics is the grammar of science.
> > >> >>>>>>> Karl Pearson
> > >> <http://en.wikipedia.org/wiki/The_Grammar_of_Science>
> > >> >>>>>>
> > >> >>>>>>
> > >> >>>>>> [[alternative HTML version deleted]]
> > >> >>>>>>
> > >> >>>>>> _______________________________________________
> > >> >>>>>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org
> >
> > >> mailing list
> > >> >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >> >>>
> > >> >>>
> > >> >>> [[alternative HTML version deleted]]
> > >> >>>
> > >> >>> _______________________________________________
> > >> >>> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
> > >> mailing list
> > >> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >> >>
> > >> >>
> > >> >> _______________________________________________
> > >> >> Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
> > >> mailing list
> > >> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >> >>
> > >> >
> > >> > --
> > >> > 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 <mailto:hpa...@fredhutch.org>
> > >> > Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
> > >> > Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
> > >> >
> > >> >
> > >> > _______________________________________________
> > >> > Bioc-devel@r-project.org <mailto:Bioc-devel@r-project.org>
> > >> mailing list
> > >> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > >>
> > >>
> > >
> > > --
> > > 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
> >
>
>
>
> --
> Gabriel Becker, Ph.D
> Computational Biologist
> Genentech Research
>
> [[alternative HTML version deleted]]
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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