I am doing KEGG enrichment analysis for a non-model organism. First I annotate the genome using KAAS and I got ko numbers associated with each gene (
K11968 BANY.1.2.t00001 K04834 BANY.1.2.t00003 K13273 BANY.1.2.t00007 K04497 BANY.1.2.t00010 K09210 BANY.1.2.t00011 K10360 BANY.1.2.t00012 K10360 BANY.1.2.t00013
Then I have a list of DE genes (
gene) and performed KEGG enrichment using clusterprofiler:
x <- enricher(gene,TERM2GENE=kegg2gene,pvalueCutoff = 0.05, pAdjustMethod = "BH",qvalueCutoff = 0.05)
Then I got a list of enriched ko numbers, then how do I translate the ko numbers to pathway names/descriptions?
I know I can add
TERM2NAME=kegg2name, but how do I get a list of all kegg numbers vs names?