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ben-laufer / DMRichR

A R package and executable for the preprocessing, statistical analysis, and downstream testing and visualization of differentially methylated regions (DMRs) from CpG count matrices (Bismark cytosine reports)
https://www.benlaufer.com/DMRichR/
MIT License
39 stars 22 forks source link

Using newer Ontology for enrichR #75

Closed dlabuz closed 11 months ago

dlabuz commented 11 months ago

When I use the default ontology databases for the enrichR program it works fine:

(dbs <- c("GO_Biological_Process_2018",
+                  "GO_Cellular_Component_2018",
+                  "GO_Molecular_Function_2018",
+                  "KEGG_2019_Human",
+                  "Panther_2016",
+                  "Reactome_2016",
+                  "RNA-Seq_Disease_Gene_and_Drug_Signatures_from_GEO")

If I change the databases to it doesn't work:

dbs <- c("GO_Biological_Process_2023",
+                  "GO_Cellular_Component_2023",
+                  "GO_Molecular_Function_2023",
+                  "KEGG_2021_Human",
+                  "Reactome_2022")Running enrichR

Welcome to enrichR Checking connection ... Enrichr ... Connection is Live! FlyEnrichr ... Connection is Live! WormEnrichr ... Connection is Live! YeastEnrichr ... Connection is Live! FishEnrichr ... Connection is Live! OxEnrichr ... Connection is Live! Annotating 13461 regions from hg38 with gene symbols Building CpG islands... Building CpG shores...
Building CpG shelves... Building inter-CpG-islands... 'select()' returned 1:many mapping between keys and columns Uploading data to Enrichr... Done. Querying GO_Biological_Process_2023... Done. Querying GO_Cellular_Component_2023... Done. Querying GO_Molecular_Function_2023... Done. Querying KEGG_2021_Human... Done. Querying Reactome_2022... Done. Parsing results... Done. Submiting results from enrichR to rrvgo... Warning: enrichR did not finish. The website may be down or there are internet connection issues.

Is there an issue with rrvgo and new ontology databases? I am working with a human dataset

It seems to get to this line and stop as I get the previous file "Ontologies/enrichr.xlsx" but nothing else after: 

        DMRichR::slimGO(tool = "enrichR",
                        annoDb = annoDb,
                        plots = FALSE) %T>%
        openxlsx::write.xlsx(file = glue::glue("Ontologies/enrichr_slimmed_results.xlsx")) %>%
dlabuz commented 11 months ago

Changed the values in the geneOntology.R script at slimGO line as well as DM.R script and seems to work