[Bioc-devel] chromosome lengths (seqinfo) for supported BSgenome builds into GenomeInfoDb?
Michael Lawrence
lawrence.michael at gene.com
Fri Jun 5 22:46:10 CEST 2015
Not a big fan of the gets (<-) syntax for "verb" functions.
standardizeSeqinfo() is probably the most "proper" name according to
our nomenclature. But novice users are still just going to want to do
genome(gr) <- "hg19" and have it just the right thing.
On Fri, Jun 5, 2015 at 1:36 PM, Hervé Pagès <hpages at fredhutch.org> wrote:
> On 06/05/2015 01:19 PM, Michael Lawrence wrote:
>>
>> To support the multi-genome case, one could set the genome as a
>> vector, one value for each seqname, and it would fix the
>> style/seqlength per seqname. It could sort by the combination of
>> seqname and species. Presumably it would do nothing for unknown
>> genomes.
>>
>> But I agree that a standardizeSeqinfo() that amounts to "genome(x) <-
>> genome(x)" would make sense.
>>
>> I don't think people sort too often by seqnames (except to the
>> "natural" ordering),
>
>
> That's what sort(), order(), rank() do by default: they sort by seqnames
> first, then by start, then by end, and finally by strand.
>
>> but I could be wrong. I do sympathize though with
>> the need for a low-level accessor. At least one would want a parameter
>> for disabling the standardization.
>
>
> Ok. So the candidates are:
>
> (a) standardizeSeqinfo(gr) <- "hg19"
>
> (b) gr <- standardizeSeqinfo(gr, "hg19")
>
> (c) standardizeGenome(gr) <- "hg19"
>
> (d) gr <- standardizeGenome(gr, "hg19")
>
> (e) seqinfo(gr) <- "hg19"
>
> Is there a risk of confusion with keepStandardChromosomes where
> "standard" means a very different thing? I'll add 2 more:
>
> (f) normalizeSeqinfo(gr) <- "hg19"
>
> (g) gr <- normalizeSeqinfo(gr, "hg19")
>
> Anyway, we're not here yet. As pointed in an earlier post, there are
> still some missing pieces to complete the puzzle.
>
> Thanks,
>
> H.
>
>>
>> On Fri, Jun 5, 2015 at 12:54 PM, Kasper Daniel Hansen
>> <kasperdanielhansen at gmail.com> wrote:
>>>
>>> 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.gabe at 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.michael at gene.com
>>>>>
>>>>> wrote:
>>>>
>>>>
>>>>> On Thu, Jun 4, 2015 at 11:48 PM, Hervé Pagès <hpages at 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.michael at gene.com <mailto:lawrence.michael at 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
>>>>>>> <hpages at fredhutch.org
>>>>>>> <mailto:hpages at 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
>>>>>>> <stvjc at channing.harvard.edu <mailto:stvjc at 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.triche at gmail.com <mailto:tim.triche at 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
>>>>>>> >>>> <stvjc at channing.harvard.edu <mailto:
>>>>>
>>>>> stvjc at 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 <
>>>>>>> >>>>> kasperdanielhansen at gmail.com
>>>>>>> <mailto:kasperdanielhansen at 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.triche at gmail.com <mailto:tim.triche at 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 at r-project.org
>>>>>>> <mailto:Bioc-devel at r-project.org>
>>>>>>> mailing list
>>>>>>> >>>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>> >>>
>>>>>>> >>>
>>>>>>> >>> [[alternative HTML version deleted]]
>>>>>>> >>>
>>>>>>> >>> _______________________________________________
>>>>>>> >>> Bioc-devel at r-project.org <mailto:Bioc-devel at r-project.org>
>>>>>>> mailing list
>>>>>>> >>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>>>> >>
>>>>>>> >>
>>>>>>> >> _______________________________________________
>>>>>>> >> Bioc-devel at r-project.org <mailto:Bioc-devel at 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: hpages at fredhutch.org <mailto:hpages at fredhutch.org>
>>>>>>> > Phone: (206) 667-5791 <tel:%28206%29%20667-5791>
>>>>>>> > Fax: (206) 667-1319 <tel:%28206%29%20667-1319>
>>>>>>> >
>>>>>>> >
>>>>>>> > _______________________________________________
>>>>>>> > Bioc-devel at r-project.org <mailto:Bioc-devel at 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: hpages at fredhutch.org
>>>>>> Phone: (206) 667-5791
>>>>>> Fax: (206) 667-1319
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioc-devel at 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 at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>>
>>
>> _______________________________________________
>> Bioc-devel at 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: hpages at fredhutch.org
> Phone: (206) 667-5791
> Fax: (206) 667-1319
More information about the Bioc-devel
mailing list