[BioC] Help with loading newly created custom annotation db into R session

Ochsner, Scott A sochsner at bcm.tmc.edu
Mon Jan 5 17:44:10 CET 2009

Dear list,

How do I load a custom annotation package into an R session?  I've created a custom annotation database by following the steps laid out in the SQLForge vignette using the gui version of R with windows XP.  Up until now, all I've had to do to load an annotation package into an R session is to use the
convenient drop down menus within the gui to retrieve the package from BioC followed by library(package name.db).  I am at a loss as to what to do with the new annotation package I've created which is sitting on my desktop.  I know I need to place the file into the correct path, I'm just not sure
where or how.  I've looked at the list serve but have been unable to find a thread dealing with what I feel is probably a no brainer to most users.

> library(AnnotationDbi) 
> openVignette()
> read.table("C:\\DOCUME~1\\sochsner\\Desktop\\ZcustomIDs.txt",header=F)[1:5,]
               V1     V2
1 DR_UNI_CAND_A01  57935
2 DR_UNI_CAND_A01  57935
3 DR_UNI_CAND_A02 402842
4 DR_UNI_CAND_A02 402842
5 DR_UNI_CAND_A03 493624
> ZcustomIDs<-"C:\\DOCUME~1\\sochsner\\Desktop\\ZcustomIDs.txt"
> makeZEBRAFISHCHIP_DB(affy=FALSE,prefix="Zcustom",fileName=ZcustomIDs,baseMapType="eg",outputDir="C:\\DOCUME~1\\sochsner\\Desktop",version="1.0.0",manufacturer="custom",chipName="Zebrafish custom array")
Loading required package: RSQLite
Loading required package: DBI
baseMapType is eg
Prepending Metadata
Creating Genes table
Appending Probes
Found 0 Probe Accessions
Appending Gene Info
Found 4401 Gene Names
Found 4401 Gene Symbols
Appending Chromosomes
Appending RefSeq
Appending Pubmed
Appending Unigene
Appending ChrLengths
Appending 3 GO tables
Appending 3 GO ALL tables
Appending KEGG
Appending EC
Appending Chromosome Locations
Appending Pfam
Appending Prosite
Appending Alias
Appending Ensembl
Appending Uniprot
Appending Zfin
Appending Metadata 

Creating package in C:\DOCUME~1\sochsner\Desktop/Zcustom.db
> sessionInfo()
R version 2.8.0 (2008-10-20) 

LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252

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

other attached packages:
[1] RSQLite_0.7-1       DBI_0.2-4           zebrafish.db0_2.2.5 AnnotationDbi_1.4.0 Biobase_2.2.0 

Scott A. Ochsner, Ph.D.
Molecular and Cellular Biology
Baylor College of Medicine
Houston, TX. 77030
phone: 713-798-6227 

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