PFAM Enrichment in GOstats
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@iain-gallagher-2532
Last seen 8.6 years ago
United Kingdom

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 
PFAM Category GOstats • 2.0k views
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@james-w-macdonald-5106
Last seen 2 days ago
United States

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.

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Thanks James

I'll try again tomorrow.

Best,

iain

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@iain-gallagher-2532
Last seen 8.6 years ago
United Kingdom

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 
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Ugh. My fix was thiiis close to being correct, but I added in an extra period. Sorry about that. I'll upload the fix and you can get the update tomorrow.

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Or send me your email address (to jmacdon AT uw.edu) and I will email you the fixed version.

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Thanks James.

I can wait until tomorrow :)

best,

iain

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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 5 months ago
China/Guangzhou/Southern Medical Univer…

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

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Thanks, I'll check this out today. Think I have used the package in the past anyway.

best,

iain

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