Question: #clusterProfiler# KEGG enrichment with non-reference species
0
3.0 years ago by
googneed0
googneed0 wrote:

Dear all,

I have some rna-seq data with no reference genome. I got the ko number using the transcript sequences by kaas online servers. I want to know whether the package "clusterProfiler" cound handle the ko numbers to show me the kegg enrichment, or are there some other software/packages instead?

Any infomartion is much appreciated.

modified 2.1 years ago by renuka.nayak0 • written 3.0 years ago by googneed0
Answer: #clusterProfiler# KEGG enrichment with non-reference species
2
3.0 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

you can use enrichKEGG function with input genes of K numbers and organism="ko".

Great！ It works! Thx!

Answer: #clusterProfiler# KEGG enrichment with non-reference species
0
2.1 years ago by
renuka.nayak0 wrote:

Can you please also clarify what is being used to generate the numbers in the the GeneRatio and BgRatio columns in this case where organism is set to "ko"?

And is there a way to specify a user-specified set of background KO numbers?