Dear all,

I try to use ClusterProfiler for Enrichment Analysis (KEGG). I face a problem right I try to create gseKEGG object. In the instructions there is said "organism KEGG Organism Code: The full list is here: https://www.genome.jp/kegg/catalog/org_list.html (need the 3 letter code)"

My problem is that my organism has four letter code "pfre" (Propionibacterium freudenreichii subsp. freudenreichii DSM 20271).

Is there anything what I could do to have the analysis for my organism?

kegg_organism = "pfre"
kk2 <- gseKEGG(geneList     = gene_list,
               organism     = pfre,
               nPerm        = 10000,
               minGSSize    = 3,
               maxGSSize    = 800,
               pvalueCutoff = 0.05,
               pAdjustMethod = "none",
               keyType       = "kegg")


Error in organismMapper(organism) : object 'pfre' not found

When you ran the function you used pfre without quotes or using your defined kegg_organism ... could you try running

kegg_organism = "pfre"
kk2 <- gseKEGG(geneList     = gene_list,
               organism     = "pfre",    # or  organism = kegg_organism 
               nPerm        = 10000,
               minGSSize    = 3,
               maxGSSize    = 800,
               pvalueCutoff = 0.05,
               pAdjustMethod = "none",
               keyType       = "kegg")