Dear list,

I am trying to create Arabidopsis mappings from genes to Pfam-profiles,
because these are not included in the default annotation package.

Thus I have downloaded the mappings from IPI and generated a table with
column1 the gene id and column 2 the Pfam profiles, and dropped this table
into a SQLite-file (Pfam.sqlite) using the RSQLite package. In the end I
would like to link this information to a normal annotation package for
Arabidopsis but would also be happy to generate a separate Pfam-Annotation
package only. My first approach using the makeAnnDbPkg failed due to an
error (see below)… Any suggestions?

>myPath <- getwd()
> seed <- new("AnnDbPkgSeed", Package="ATHPfam", Version="1.0",
AnnObjPrefix="ATHPfam")
> makeAnnDbPkg(seed, dbfile="Pfam.sqlite", dest_dir=myPath, no.man=TRUE)
Error in sqliteExecStatement(con, statement, bind.data) :
  RS-DBI driver: (error in statement: no such table: metadata)

> sessionInfo()
R version 2.7.0 (2008-04-22)
i386-apple-darwin8.10.1

locale:
en_IE.UTF-8/en_IE.UTF-8/C/C/en_IE.UTF-8/en_IE.UTF-8

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
base

other attached packages:
[1] AnnotationDbi_1.2.0 Biobase_2.0.1       RSQLite_0.6-8       DBI_0.2-4

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