Hello list

The GOstats vignette suggests it's possible to test for PFAM category enrichment using a PFAMHyperGParams instance, and indeed I've done this in the past.

Today however I'm getting the following error:

#make hyperGParams object
params<-new("PFAMHyperGParams", geneIds = goiEG, universeGeneIds = universe, annotation = "org.Mm.eg.db", pvalueCutoff = 0.05, testDirection = "over")

#perform the test
hgOver <- hyperGTest(params)

Error in .testForValidKeytype(x, keytype) :
  Invalid keytype: PROBEID. Please use the keytypes method to see a listing of valid arguments.

My geneIds and universeGeneIds are both made up of EntrezGene IDs but I assume that somewhere in the code there's a line querying the PFAM.db for PROBEID?

Thanks for any help.

Best,

Iain

> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04 LTS

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8       
 [4] LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] PFAM.db_3.1.2        org.Mm.eg.db_3.1.2   GOstats_2.34.0       graph_1.46.0        
 [5] Category_2.34.0      GO.db_3.1.2          RSQLite_1.0.0        DBI_0.3.1           
 [9] AnnotationDbi_1.30.1 GenomeInfoDb_1.4.0   IRanges_2.2.1        S4Vectors_0.6.0     
[13] Matrix_1.2-0         Biobase_2.28.0       BiocGenerics_0.14.0

loaded via a namespace (and not attached):
 [1] lattice_0.20-31        XML_3.98-1.1           AnnotationForge_1.10.1 RBGL_1.44.0           
 [5] grid_3.2.0             xtable_1.8-0           GSEABase_1.30.1        genefilter_1.50.0     
 [9] annotate_1.46.0        splines_3.2.0          tools_3.2.0            survival_2.38-1 

Hi Iain,

Thanks for the bug report. This has been fixed in both release and devel versions of the Category package (version 2.34.1). The updated versions usually take about 24 hours to propagate to the download server.

Hi James (& others)

I'm getting the same error with the new Category package.

> hgOver <- hyperGTest(params)
Error in .testForValidKeytype(x, keytype) :
  Invalid keytype: PROBEID. Please use the keytypes method to see a listing of valid arguments.
> sessionInfo()
R version 3.2.0 (2015-04-16)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04 LTS

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C               LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8   
 [6] LC_MESSAGES=en_GB.UTF-8    LC_PAPER=en_GB.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] org.Mm.eg.db_3.1.2   GOstats_2.34.0       graph_1.46.0         Category_2.34.1      GO.db_3.1.2          RSQLite_1.0.0       
 [7] DBI_0.3.1            AnnotationDbi_1.30.1 GenomeInfoDb_1.4.0   IRanges_2.2.1        S4Vectors_0.6.0      Matrix_1.2-0        
[13] Biobase_2.28.0       BiocGenerics_0.14.0

loaded via a namespace (and not attached):
 [1] lattice_0.20-31        XML_3.98-1.1           AnnotationForge_1.10.1 RBGL_1.44.0            grid_3.2.0             xtable_1.7-4          
 [7] GSEABase_1.30.1        genefilter_1.50.0      annotate_1.46.0        splines_3.2.0          tools_3.2.0            survival_2.38-1 

clusterProfiler can also be used to test PFAM， see http://ygc.name/2015/05/11/use-clusterprofiler-as-an-universal-enrichment-analysis-tool/