[BioC] problem with GOHyperGParams in package Category

[Mark W Kimpel]

Tonight I set about to generalize a function I had written to do GO 
analysis using the package GOstats, and to do this by switching to 
package Category. I wanted to add KEGG testing to the GO testing I have 
been doing. All I did to my code was to add a conditional such that if 
the category was KEGG a KEGGHyperGParams object would be created, else 
if it was BP, MF, or CC a GOHyperGParams object would be created. Then 
the object params would be tested. I did not change my GOHyperGParams 
generating code and, curiously, the KEGG option works beautifully. 
However, whenever I use a GO category I get a strange error message (see 
below for this and sessionInfo. I seem to remember something odd like 
this happening when some objects with the same name collided, but I'm 
not sure how that could be happening.

Output is below, help is appreciated.

Mark

######################
#my code: CatToTest is either "KEGG", "BP, "MF, or "CC".

if (CatToTest == "KEGG"){
   params <- new("KEGGHyperGParams", geneIds = selectedEntrezIds,
               universeGeneIds = entrez.universe.vec,
                annotation = annotationPckg,
               pvalueCutoff = hgCutoff, testDirection = testDirection)
} else {
   params <- new("GOHyperGParams", geneIds = selectedEntrezIds,
               universeGeneIds = entrez.universe.vec,
               annotation =  annotationPckg,
               ontology = CatToTest, pvalueCutoff = hgCutoff,
               conditional = TRUE, testDirection = testDirection)
}

test.obj<-hyperGTest(params)
######################################
# error out
GO.out <- Cat.anal.func(CatToTest = Cats[i],
Error in getClass(Class, where = topenv(parent.frame())) :
   c("\"GOHyperGResult\" is not a defined class", "\"BPHyperGResult\" is 
not a defined class")

Enter a frame number, or 0 to exit

  1: Cat.anal.func(CatToTest = Cats[i], input.df = pcmt1.cor.nodes, 
annotationPc
  2: CatHyperMaxCats.func(CatToTest, optimizedParam)
  3: hyperGTest(params)
  4: .valueClassTest(standardGeneric("hyperGTest"), "HyperGResultBase", 
"hyperGT
  5: is(object, Cl)
  6: .class1(object)
  7: .class1(object)
  8: .hyperGTestInternal(p)
  9: new(className, pvalues = stats$p[ord], oddsRatios = 
stats$odds[ord], expect
10: getClass(Class, where = topenv(parent.frame()))
############################################################
#sessionInfo()
R version 2.6.1 (2007-11-26)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

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

other attached packages:
  [1] GO.db_2.0.2         rat2302_2.0.1       qvalue_1.12.0
  [4] Category_2.4.0      genefilter_1.16.0   survival_2.34
  [7] annotate_1.16.1     xtable_1.5-2        AnnotationDbi_1.0.6
[10] RSQLite_0.6-8       DBI_0.2-4           graph_1.16.1
[13] Biobase_1.16.3

loaded via a namespace (and not attached):
[1] cluster_1.11.10 RBGL_1.14.0



-- 

Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 204-4202 Home (no voice mail please)

mwkimpel<at>gmail<dot>com