Question: ClusterProfiler - enrichKEGG on specific pathways
gravatar for bekah
14 months ago by
bekah20 wrote:


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?

Best wishes,


ADD COMMENTlink modified 14 months ago • written 14 months ago by bekah20
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 300 users visited in the last hour