I have blasted the genes of my non-model organism using the KEGG blastKOALA - so have a list of k numbers associated with my genes. I am using clusterprofiler to run enrichment to see which pathways are significantly enriched. I tried against mze, but it said no genes could be mapped, so I tried using ko and this seemed to work? are the k numbers specific to an organism? As I'm sure when I looked at the results from blastKOALA the majority of top hits were mze, which is also a cichlid fish?
My code is:
kk<-enrichKEGG(gene=kolist$KeggID, organism='ko', keyType="kegg",pvalueCutoff = 0.1, pAdjustMethod = "fdr", qvalueCutoff = 0.05, universe = backlist$KEGGID)
Using KO means a lot of irrelevant pathways are also included in the enrichment analysis e.g. human diseases.
Is there a way of selecting specific pathways to include in the analysis/omitting irrelevant pathways please?