ClusterProfiler - enrichKEGG on specific pathways
0
0
Entering edit mode
bekah ▴ 40
@bekah-12633
Last seen 5.7 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 • 1.8k views
ADD COMMENT
0
Entering edit mode

Hey bekah, I wonder if you have found the solution to solve this issue? Best wishes, EvaLan

ADD REPLY

Login before adding your answer.

Traffic: 639 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6