ClusterProfiler - enrichKEGG on specific pathways
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bekah ▴ 20
@bekah-12633
Last seen 3.9 years ago

Hiya,

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,

Rebekah

kegg enrichkegg clusterprofiler • 840 views