[Bioc-devel] Request for Comment: SNP Annotation package design

Sean Davis sdavis2 at mail.nih.gov
Wed Feb 15 20:53:35 CET 2006


It seems like there is more information available than that in your proposed
table structure.  Do you really want to drop those accessory data (like Avg
Het. or from what database the snps are derived)?  If you stuck with the
table structure from UCSC, then on the implementation side of things, one
could envision being able to use RMySQL, RSQLite, or RdbiPgSQL to access the
tables which could be easily obtained from bioc (RSQLite) or via a local
database (which probably several of us already have running).  I don't do
much SNP work, so I shouldn't really be saying much, but disk space is
pretty cheap, so it seems like more might be better (or at least not worse)


On 2/15/06 2:02 PM, "Seth Falcon" <sfalcon at fhcrc.org> wrote:

> Greetings all,
> Some of us have been working on a design for annotation packages for
> SNP chips.
> We would like to get input from the community at large.  A summary of
> our current design notes is available here:
> http://wiki.fhcrc.org/bioc/SNP_Annotation_Package_Discussion
> You can comment either by replying to this thread or creating an
> account on the wiki (see above URL) and adding comments directly to
> the page.  Adding to the wiki directly is preferred.
> We will let the discussion evolve for 1 week before beginning
> implementation work.
> Best Wishes,
> + seth
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