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Question: PFAM Enrichment in GOstats
0
gravatar for Iain Gallagher
3.3 years ago by
United Kingdom
Iain Gallagher910 wrote:

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 
ADD COMMENTlink modified 3.3 years ago by Guangchuang Yu1.0k • written 3.3 years ago by Iain Gallagher910
0
gravatar for James W. MacDonald
3.3 years ago by
United States
James W. MacDonald47k wrote:

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.

ADD COMMENTlink written 3.3 years ago by James W. MacDonald47k

Thanks James

I'll try again tomorrow.

Best,

iain

ADD REPLYlink written 3.3 years ago by Iain Gallagher910
0
gravatar for Iain Gallagher
3.3 years ago by
United Kingdom
Iain Gallagher910 wrote:

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 
ADD COMMENTlink written 3.3 years ago by Iain Gallagher910

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.

ADD REPLYlink written 3.3 years ago by James W. MacDonald47k

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

ADD REPLYlink written 3.3 years ago by James W. MacDonald47k

Thanks James.

I can wait until tomorrow :)

best,

iain

ADD REPLYlink written 3.3 years ago by Iain Gallagher910
0
gravatar for Guangchuang Yu
3.3 years ago by
Guangchuang Yu1.0k
Hong Kong
Guangchuang Yu1.0k wrote:

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

ADD COMMENTlink written 3.3 years ago by Guangchuang Yu1.0k

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

best,

iain

ADD REPLYlink written 3.3 years ago by Iain Gallagher910
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