Hi Vince,
The current Homo.sapiens package/object contains a reference to an hg19
TranscriptDb object (which makes it specific to hg19). But you can
easily make a custom Homo.sapiens object of your own that points to a
custom TranscriptDb object. Making a custom OrganismDbi object is easy
to do and is documented in the OrganismDbi vignette:
http://www.bioconductor.org/packages/devel/bioc/vignettes/OrganismDbi/inst/doc/OrganismDbi.pdf
So there nothing very fancy going on here right now. But you can
customize to match a build if you have made the base annotation objects
(TranscriptDb, OrgDb etc.).
Marc
On 07/28/2014 10:37 AM, Vincent Carey wrote:
I confirmed that the rtracklayer liftOver will work with the appropriate
chain. the
remap utility seems to have some more configurability. might be worth a
look.
What I need to do promptly is put the proper seqinfo on result of
makeCurrentGwascat
so that folks are not led astray. We also need good marking of which build
is in use on all our ranges, IMHO.
On Mon, Jul 28, 2014 at 1:14 PM, Vincent Carey <st...@channing.harvard.edu>
wrote:
I just noticed that the addresses for NHGRI GWAS catalog distribution
are relative to GRCh38. Is there a plan for using Homo.sapiens with
selection of build? It may not be uncommon for someone to want to
work with different builds.
What would be useful for me at this time is a simple way to get a Seqinfo
structure respecting GRCh38. Also, liftOver seems to have been replaced
by NCBI remap. Apparently the new build can also be called hg38, and a
chain
file exists, so rtracklayer liftOver utility should still succeed.
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