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