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"EXTID2PATHID" error in DOSE #86

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carlossainz813 opened this issue Dec 18, 2024 · 0 comments
Open

"EXTID2PATHID" error in DOSE #86

carlossainz813 opened this issue Dec 18, 2024 · 0 comments

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@carlossainz813
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I've been having an issue with the DOSE package, specifically with the functions that call on Disease Ontology (enrichDO, and gseDO).
This is the code that I have been using.

          library(DOSE)  
          library(org.Hs.eg.db)  
          library(clusterProfiler)  
          
          data(geneList)  
          
          gene <- names(geneList)[abs(geneList) > 1.5]  
          head(gene)  
          
          x <- enrichDO(gene          = gene,  
                        ont           = "HDO",  
                        organism = "hsa",  
                        pvalueCutoff  = 0.05,  
                        pAdjustMethod = "BH",  
                        universe      = names(geneList),  
                        readable      = FALSE)

However, whenever I run the code I get this error:
Error in get("EXTID2PATHID", envir = USER_DATA) :
object 'EXTID2PATHID' not found

I am unsure what is happening, as it used to work before, but now it gives me this error directly. I've tried uninstalling and reinstalling DOSE and all its dependencies but haven't managed to solve the issue.

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