Entering edit mode
Mark W Kimpel
▴
830
@mark-w-kimpel-2027
Last seen 10.2 years ago
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
