[Bioc-devel] Update on SQLite-based annotation data package (prototype available)

[Seth Falcon]

Vincent Carey 525-2265 <stvjc at channing.harvard.edu> writes:

>>
>>   2. More flexible queries.  With the SQLite-based packages, many
>>      queries that currently require loops over possible many entire
>>      environments can be accomplished in one statement.  Using some
>>      simple SQL statements, I've been able to improve the performance
>>      of the hyperGTest function by 10x.  Focused queries will
>>      generally be much faster with the SQLite-based packages.
>
> do we need a sql tutorial doc (i know there are plenty on the
> web but perhaps some that are focused on the types of queries to
> be used here?)  helper code that 'translates' R-like actions to
> SQL may be feasible for some of the more common tasks.

I'm hoping that an alternative API will solidify Real Soon Now.  I
would much prefer promoting a well documented API than raw SQL.  Using
raw SQL is effective, but relies on the schema definition.

But perhaps my comments are orthogonal to your suggestion.  A SQL
tutorial with "translations" of R concepts is a great idea.

+ seth