[Bioc-devel] naming of TxDb packages

Hi Michael,
We're actually using a patched version of makeTranscriptDbFromBiomart to
get models out of an internal biomart.  Patch is on its way to Marc.

So it would be like: TxDb.Hsapiens.BioMart.hg19.gneGenes?
This suggests that you have a Mart called "hg19" (see below why).
Seems weird to mix the technical mode of data retrieval into the name.
The naming scheme when 'Data source' is "BioMart" seems to be a little
bit different. For example, if I use makeTranscriptDbFromBiomart() with
biomart="ensembl" and dataset="hsapiens_gene_ensembl", then I get:

   > GenomicFeatures:::.makePackageName(txdb)
   [1] "TxDb.Hsapiens.BioMart.ensembl.GRCh37.p5"

Token #4 ("ensembl") is the name of the Mart. I'm a little bit
surprised with token #5 though. I would have expected it to be
the ensembl version (eventually followed by the reference genome)
because one can always infer the reference genome from the ensembl
version but not the other way around. In other words, if Ensembl
makes 2 or more releases based on the same reference genome, our
current naming scheme won't differentiate the 2 TxDb packages.
Wouldn't it be better if we had something like:

   TxDb.Hsapiens.BioMart.ensembl.63
   TxDb.Hsapiens.BioMart.ensembl.64

Anyway, back to your problem. Yes in your case the technical mode
doesn't really matter so it's really up to you. Maybe being explicit
about the reference genome (with *.UCSC.hg19.*) is more important
than the technical mode?

H.
Michael

2011/11/3 Herv? Pag?s <hpages at fhcrc.org <mailto:hpages at fhcrc.org>>

    Hi Michael,

    On 11-11-02 08:58 PM, Michael Lawrence wrote:

        What are the precise meanings of the tokens in the TxDb package
        names. In
        particular, is "UCSC" the genome provider or the annotation
        provider? In
        the official packages, those are one in the same, but if someone
        wanted to
        make a package for custom annotations on a UCSC genome?

    The pkg name is generated automatically by internal helper function
    GenomicFeatures:::.__makePackageName(). This function extracts all the
    tokens from the txdb's metadata table. It looks like the 3rd token
    in the pkg name is extracted from the 'Data source' field and can only
    be "UCSC" or "BioMart", typically indicating whether the txdb was made
    with makeTranscriptDbFromUCSC() or makeTranscriptDbFromBiomart().
    The first function downloads annotations from the UCSC genome
    browser using rtracklayer. The 2nd one downloads them with biomaRt
    from whatever mart/dataset was specified.

    For your custom annotations, the final name of the pkg will depend on
    what GenomicFeatures:::.__makePackageName() finds in the metadata
    table of your txdb, but, if 'Data source' is not "UCSC" or "BioMart",
    it seems that GenomicFeatures:::.__makePackageName() will fail (and not
    in a very informative way I'm afraid). If I understand correctly, you
    are making your custom txdb object with a call to makeTranscriptDb()?
    If that's the case, make sure you provide enough information
    thru its 'metadata' argument. Maybe you could set 'Data source' to
    "UCSC" and use some kind of custom name for the table (which in your
    case is probably not a real UCSC "table"). This custom name will become
    the last token in the package name. So you would end up with something
    like:

      TxDb.Hsapiens.UCSC.hg19.__GenentechGenes

    This solution would have the advantage of having
    GenomicFeatures:::.__makePackageName() work out-of-the-box.
    But maybe it's confusing because it suggests that
    the txdb was made with makeTranscriptDbFromUCSC()? I hope
    it's not.

    H.

        Thanks,
        Michael

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    Herv? Pag?s

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    Division of Public Health Sciences
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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 fhcrc.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319

[Bioc-devel] naming of TxDb packages

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