[BioC] Using GOstats for a non-model organism

[Maureen J. Donlin]

Hi all,

I'm new to R and have some very basic questions about using GOstats with 
a non-model organism.
I'm trying to use the tutorial by Marc Carlson "How to Use GOstats 
and...with unsupported model organisms."

I've created a GO to gene mapping file with the following 3 columns of data:
Goterm    Evidence    GeneID
GO:0015893    IEA    CNAG_00003
GO:0043231    IEA    CNAG_00003
GO:0015203    IEA    CNAG_00003
GO:0044425    IEA    CNAG_00003
...

I can import it using read.table, but I don't seem to be able to invoke 
the data frame correctly.

The tutorial reads:
library("org.Hs.eg.db")
frame = toTable(org.Hs.egGO)
goFrameData = data.frame(frame$go_id, frame$Evidence, frame$gene_id)

I imported the data into an object using read.table
 >CneoGOanno <- read.table("Cneo_GOannot.txt")

I tried to create a frame using:
 > frame = toTable(CneoGOannot)
Error in function (classes, fdef, mtable)  :
   unable to find an inherited method for function "toTable", for 
signature "data.frame"

Do I have to create some sort of database for this organism first?  If 
so, what is it's format?

Any suggestions would be most appreciated.

Regards,
Maureen Donlin

At the risk of too long of an email, here's the session info:
 > sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] org.Hs.eg.db_2.4.6   GOstats_2.16.0       RSQLite_0.9-4        
DBI_0.2-5            graph_1.28.0         Category_2.16.0      
AnnotationDbi_1.12.0
[8] Biobase_2.10.0

loaded via a namespace (and not attached):
  [1] annotate_1.28.0   genefilter_1.32.0 GO.db_2.4.5       
GSEABase_1.12.2   RBGL_1.26.0       splines_2.12.1    survival_2.36-2   
tools_2.12.1
  [9] XML_3.2-0         xtable_1.5-6


-- 

Maureen J. Donlin, Ph.D.
Research Associate Professor

Dept. of Molecular Microbiology&  Immunology
Dept. of Biochemistry&  Molecular Biology
Saint Louis University School of Medicine
507 Doisy Research Center
1100 S. Grand
St. Louis, MO  63104
Phone: 314-977-8858