I would like to compare the GO enrichments of several gene clusters.

I tried to use goProfles and goTools.

Since I am using a non model organism I build my own organism package using AnnotationForge

> keytypes(org.Psp.FOBEG1.eg.db)

[1] "Locus"        "EnsemblNames" "GID"          "GO"           "EVIDENCE"     "ONTOLOGY"     "GOALL"        "EVIDENCEALL"  "ONTOLOGYALL" 

The central Ids of my package are GeneIDs:

> head(keys(org.Psp.FOBEG1.eg.db, keytypes="GID"))->ids
> select(org.Psp.FOBEG1.eg.db, keys=ids, columns="GO", keytype="GID")
        GID         GO
1  11588526       <NA>
2  11588527 GO:0003735
3  11588527 GO:0005840
4  11588527 GO:0006412
5  11588528 GO:0005737
6  11588528 GO:0052906
7  11588529 GO:0005840
8  11588529 GO:0006364
9  11588529 GO:0042274
10 11588529 GO:0043022
11 11588530 GO:0003735
12 11588530 GO:0005840
13 11588530 GO:0006412
14 11588531 GO:0046417
Warning message:
In .generateExtraRows(tab, keys, jointype) :
  'select' resulted in 1:many mapping between keys and return rows

Now, my problem is that I get a similar error with both goTools and goProfiles; therefore I guess I have something wrong in my org. package. The problem is that I do not really understand what I did wrong.

> basicProfile (test1, onto="ALL", level=1, orgPackage="org.Psp.FOBEG1.eg.db")

Error in eval(expr, envir, enclos) : 

  object 'org.Psp.FOBEG1.egGO' not found

> res <-ontoCompare(test1, probeType="org.Psp.FOBEG1.eg")
Starting ontoCompare...
Error in get(paste(probeType, "GO", sep = "")) : 
  object 'org.Psp.FOBEG1.egGO' not found

> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
 [1] org.Psp.FOBEG1.eg.db_0.1 hgu133a.db_2.14.0        goTools_1.38.0           goProfiles_1.26.0        GO.db_2.14.0             org.Hs.eg.db_2.14.0     
 [7] GOSemSim_1.22.0          AnnotationDbi_1.26.0     GenomeInfoDb_1.0.2       Biobase_2.24.0           BiocGenerics_0.10.0      RSQLite_0.11.4          
[13] DBI_0.3.0                Rcpp_0.11.2              BiocInstaller_1.14.2    

loaded via a namespace (and not attached):
[1] IRanges_1.22.10 stats4_3.1.1    tools_3.1.1 

Looking at the Index.html file of my package it is obvious that the org.Psp.FOBEG1.egGO is missing.

Looking in other organism packages (e.g. org.Hs.eg.db) I understood that org.Xx.egGO is a "Go3AnnDbBimap" object. 

> str(org.Hs.egGO)
Formal class 'Go3AnnDbBimap' [package "AnnotationDbi"] with 9 slots
  ..@ rightTables: Named chr [1:3] "go_bp" "go_cc" "go_mf"
  .. ..- attr(*, "names")= chr [1:3] "BP" "CC" "MF"
  ..@ L2Rchain   :List of 2
  .. ..$ :Formal class 'L2Rlink' [package "AnnotationDbi"] with 8 slots
  .. .. .. ..@ tablename   : chr "genes"
  .. .. .. ..@ Lcolname    : chr "gene_id"
  .. .. .. ..@ tagname     : chr NA
  .. .. .. ..@ Rcolname    : chr "_id"
  .. .. .. ..@ Rattribnames: chr(0)
  .. .. .. ..@ Rattrib_join: chr NA
  .. .. .. ..@ filter      : chr "1"
  .. .. .. ..@ altDB       : chr(0)
  .. ..$ :Formal class 'L2Rlink' [package "AnnotationDbi"] with 8 slots
  .. .. .. ..@ tablename   : chr(0)
  .. .. .. ..@ Lcolname    : chr "_id"
  .. .. .. ..@ tagname     : Named chr "{evidence}"
  .. .. .. .. ..- attr(*, "names")= chr "Evidence"
  .. .. .. ..@ Rcolname    : chr "go_id"
  .. .. .. ..@ Rattribnames: Named chr "NULL"
  .. .. .. .. ..- attr(*, "names")= chr "Ontology"
  .. .. .. ..@ Rattrib_join: chr NA
  .. .. .. ..@ filter      : chr "1"
  .. .. .. ..@ altDB       : chr(0)
  ..@ direction  : int 1
  ..@ Lkeys      : chr NA
  ..@ Rkeys      : chr NA
  ..@ ifnotfound : list()
  ..@ datacache  :<environment: 0x13aa5f18>
  ..@ objName    : chr "GO"
  ..@ objTarget  : chr "Human"

So I would need to create such an object for my organism and include it into the package I created.

Can anyone help me to get around this problem or provide me with useful information/links/example/tutorials?

Thanks a lot!