gofilter function ERROR: object 'topNode' not found

[yulchen810]

Hi,
I encounter an ERROR when running gofilter, the input generated from compareCluster function.
Did anyone meet this before?

[guidohooiveld]

I can reproduce this error.

The information on the help page of gofilter is rather limited, but if you run this function on the output of GO enrichment analysis of a single experiment, it becomes clear that gofilter does not work when ont=ALL. In other words, gofilter only works on the level of a specific root category (i,e, one of BP, CC or MF).

Yet, if multiple experiments are analyzed with compareCluster, this results in the error your reported, even when specifying one of the 3 root categories.... See below.

@GuangchuangYu : could you, or one of your team members, have a look at this?

> library(clusterProfiler)
> data(gcSample)
> 
> ## First apply gofilter to a single list of input genes.
> ## Doesn't work with ont=ALL, only when a specific root category is defined
> 
> yy <- enrichGO(gcSample[[1]], 'org.Hs.eg.db', ont="ALL", pvalueCutoff=0.05)
> compGO_filtered <- gofilter(yy, level=4)
Error in get_go_ontology(x) : 
  ontology should be one of 'MF', 'BP', 'CC'...
> 
> ## limit to only CC ontologies
> ## works!
> yy <- enrichGO(gcSample[[1]], 'org.Hs.eg.db', ont="CC", pvalueCutoff=0.05)
> compGO_filtered <- gofilter(yy, level=4)
> 
> 
> 
> 
> ## analyze multiple input lists with compareCluster
> compGO <- compareCluster(gcSample, fun="enrichGO",
+                      OrgDb="org.Hs.eg.db", ont="ALL", pvalueCutoff=0.05)
> compGO_filtered <- gofilter(xx, level=4)
Error in getGOLevel(ont, level) : object 'topNode' not found
> 
> ## limit to only CC ontologies
> ## still an error!
> compGO <- compareCluster(gcSample, fun="enrichGO",
+                      OrgDb="org.Hs.eg.db", ont="CC", pvalueCutoff=0.05)
> compGO_filtered <- gofilter(xx, level=4)
Error in getGOLevel(ont, level) : object 'topNode' not found
> 
> 
>