Hello everyone,

Due that I can't access REVIGO website for some reason, I've been trying to use rrvgo package. I'm working with a non-model organism, so I used Blast2GO to annotate the sequences and obtain their associated GO terms. Also, I created an OrgDbPackage with annotationForge with the following .csv files:

• gene_info: containing the accession numbers and description of each gene.
• go_terms: containing the accession numbers, GO term description and GO domain for each gene.
• gene2go: containing the accession numbers and the GO term accession.

These result in an orgDb with the following keytypes:

keytypes(org.Tsd.eg.db)
[1] "gene_name" "GID"       "GO"        "ONTOLOGY"  "TERM"  

I'm working with some RNAseq data and trying to make some sense of the data we got. So, I got a dataframe of enriched GO terms with their corresponding qvalues (called A_enrich).

go_data <- godata(annoDb = "org.Tsd.eg.db", ont="BP", keytype = "GID")
simMatrix <- calculateSimMatrix(A_enrich$GO,
                                semdata = go_data,
                                ont = "BP",
                                method = "Rel",
                                keytype = "GO",
                                orgdb = org.Tsd.eg.db)

scores <- setNames(-log10(A_enriched$qval), A_enrich$GO)

reducedTerms <- reduceSimMatrix(simMatrix = simMatrix,
                                scores = scores,
                                threshold = 0.7,
                                keytype = "GO",
                                orgdb = org.Tsd.eg.db)

However, for the last one, I got the following error, even though I specified "GO" as a keytype given that this one is a valid one from my orgDb annotation:

Error in testForValidKeytype(x, keytype): 
  Invalid keytype: GOALL. Please use the keytypes method to see a listing of valid arguments.

Any help will be very much appreciated! Thanks!