[Bioc-devel] OrganismDb package for Drosophila.melanogaster

[Pariksheet Nanda]

On Tue, Nov 15, 2016 at 7:34 PM, Martin Morgan wrote:
> On 11/15/2016 09:52 AM, Obenchain, Valerie wrote:
>> On 11/15/2016 03:32 AM, Pariksheet Nanda wrote:
>>>
>>> It would be great to have an OrganismDb package for
>>> Drosophila.melanogaster, similar to Homo.sapiens, Mus.musculus and
>>> Rattus.norvegicus.
--snip--
>>> In other words, like Rattus.norvegicus, it might be good do add a UCSC
>>> "refGene" TxDb package for dm6 as "ensGene" doesn't appear to be as
good of
>>> a candidate (at least without some ugliness)?  I was looking at
creating a
>>> dm6 UCSC "refGene" TxDb.
>>
>> You can use GenomicFeatures::makeTxDbFromUCSC() to create the TxDb. The
>> man page, ?makeTxDbFromUCSC, also has helper functions that display
>> available genomes, tables and tracks.
>
> I'm not completely sure of the result, but
>
> library(OrganismDb)
> odb = makeOrganismDbFromUCSC("dm6", tableName="refGene")
>
> might be most of the way there?

Thanks Valerie and Martin for pointing out the make*() functions!

As my lab uses the same UCSC tables frequently, I used the
make*Package() functions (namely,
GenomicFeatures::makeTxDbPackageFromUCSC and
OrganismDbi::makeOrganismPackage).

For others who run OrganismDbi::makeOrganismPackage, don't forget
to edit the generated PACKAGE file and add your new TxDb package
to "Depends".


>> Valerie

> Martin

Pariksheet

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