Hi Mark,

here's one from IlluminaHumanMethylation450k.db, where the probes have two
designs; from zzz.R, declaring that the map 'DESIGN' should map primary key
'Probe_ID' to field 'Infinium_Design_Type' found in table 'probedesign', in
order to process them correctly:

IlluminaHumanMethylation450kDESIGN <-
createSimpleBimap("probedesign","Probe_ID","Infinium_Design_Type",datacache,"DESIGN","IlluminaHumanMethylation450k.db")

where the schema for table 'probedesign' is like so:

sqlite> .sch probedesign
CREATE TABLE "probedesign"(
  row_names INT,
  Probe_ID TEXT,
  Infinium_Design_Type TEXT,
  AddressA_ID INT,
  AddressB_ID INT,
  Color_Channel,
  Random_Loci,
  Methyl27_Loci,
  Is_HMM_Island,
  NuID TEXT,
  CpGs INT,
  Coordinate_37 INT,
  Chromosome_37 TEXT,
  Coordinate_36 INT,
  Chromosome_36 TEXT,
  Genome_Build INT
);
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 Carlson's
SQLforge though... there are things about magical namespace exports that I
still don't understand.

--t

On Thu, Mar 10, 2011 at 9:02 AM, Mark Dunning <mark.dunning@gmail.com>wrote:

> Hi all,
>
> I am interested in adding some custom fields to my existing illumina
> annotation packages (basically extra information that we have gathered
> by re-annotating the probes). I have already created sqlite objects
> for the new data I intend to add. I thought that the createSimpleBimap
> function in AnnotationDbi might be an easy way to achieve this.
> However, I'm a little confused by the example in the SQLForge
> vignette:
>
>  hgu95av2NAMESYMBOL <-
>
> createSimpleBimap("gene_info","gene_name","symbol",hgu95av2.db:::datacache,"NAMESYMBOL","hgu95av2.db")
>
> This example runs fine, but I'm struggling trying to work out what is
> 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)
> [1] "accessions"   "map_counts"   "map_metadata" "metadata"     "probes"
> [6] "sqlite_stat1"
>
> Regards,
>
> Mark
>
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>



-- 
If people do not believe that mathematics is simple, it is only because they
do not realize how complicated life is.
John von Neumann<http://www-groups.dcs.st-and.ac.uk/~history/Biographies/Von_Neumann.html>

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