[Bioc-devel] Update on SQLite-based annotation data package (prototype available)
Vincent Carey 525-2265
stvjc at channing.harvard.edu
Thu Feb 1 18:01:26 CET 2007
> 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.
> + seth
> >> sessionInfo()
> > R version 2.5.0 Under development (unstable) (2007-01-22 r40543)
> > x86_64-unknown-linux-gnu
> > locale:
> > LC_CTYPE=it_IT.UTF-8;LC_NUMERIC=C;LC_TIME=it_IT.UTF-8;LC_COLLATE=it_IT.UTF-8;LC_MONETARY=it_IT.UTF-8;LC_MESSAGES=it_IT.UTF-8;LC_PAPER=it_IT.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=it_IT.UTF-8;LC_IDENTIFICATION=C
> > attached base packages:
> >  "tools" "stats" "graphics" "grDevices" "utils" "datasets"
> >  "methods" "base"
> > other attached packages:
> > hgu95av2db AnnotationDbi RSQLite DBI Biobase
> > "1.13.91" "0.0.41" "0.4-19" "0.1-12" "1.13.34"
> > fortunes
> > "1.3-2"
> > Cheers
> > Wolfgang
> >> We are making progress on converting the annotation data packages to
> >> use SQLite as the backend storage mechanism.
> >> The devel annotation package repository has a prototype of a
> >> SQLite-based annotation data package (hgu95av2db). If you are running
> >> R-devel, then you should be able to install it via biocLite (sorry,
> >> only source package at this point).
> >> The SQLite-based annotation packages depend on the AnnotationDbi
> >> package which provides an environment-like interface that should be
> >> backwards compatible. Advanced users can get a connection to the DB
> >> and issue raw SQL queries. We are also planning to provide more
> >> convenience/accessor functions along the lines of the annotate
> >> package.
> >> Our plan for the upcoming 2.0 release of Bioconductor is to include
> >> both environment-based and SQLite-based annotation packages.
> >> If you maintain a package that makes use of annotation data packages,
> >> it would be good to see if the hgu95av2db prototype will work with
> >> your code (if not, please let us know).
> >> + seth
> >> _______________________________________________
> >> Bioc-devel at stat.math.ethz.ch mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > --
> > ------------------------------------------------------------------
> > Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber
> Bioc-devel at stat.math.ethz.ch mailing list
More information about the Bioc-devel