here's one from IlluminaHumanMethylation450k.db, where the probes have
designs; from zzz.R, declaring that the map 'DESIGN' should map
'Probe_ID' to field 'Infinium_Design_Type' found in table
order to process them correctly:
where the schema for table 'probedesign' is like so:
sqlite> .sch probedesign
CREATE TABLE "probedesign"(
CREATE INDEX Dchannel ON probedesign(Color_Channel);
CREATE INDEX Ddesign ON probedesign(Infinium_Design_Type);
Hope this helps. Some of the darker incantations are up to Marc
SQLforge though... there are things about magical namespace exports
still don't understand.
On Thu, Mar 10, 2011 at 9:02 AM, Mark Dunning
> Hi all,
> I am interested in adding some custom fields to my existing illumina
> annotation packages (basically extra information that we have
> by re-annotating the probes). I have already created sqlite objects
> for the new data I intend to add. I thought that the
> function in AnnotationDbi might be an easy way to achieve this.
> However, I'm a little confused by the example in the SQLForge
> hgu95av2NAMESYMBOL <-
> This example runs fine, but I'm struggling trying to work out what
> going on. Specifically, what is 'gene_info' are where does it get
> these data from? My guess was that it would be a table somewhere in
> the datacache object but it doesn't appear in the listing
> > tmpcon = get("dbconn", hgu95av2.db:::datacache)
> > dbListTables(tmpcon)
>  "accessions" "map_counts" "map_metadata" "metadata"
>  "sqlite_stat1"
> Bioconductor mailing list
> Search the archives:
If people do not believe that mathematics is simple, it is only
do not realize how complicated life is.
John von Neumann<http: www-groups.dcs.st-="" and.ac.uk="" ~history="" biographies="" von_neumann.html="">
[[alternative HTML version deleted]]