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Question: #clusterProfiler# KEGG enrichment with non-reference species
0
gravatar for googneed
2.1 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.

ADD COMMENTlink modified 15 months ago by renuka.nayak0 • written 2.1 years ago by googneed0
2
gravatar for Guangchuang Yu
2.1 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"`.

ADD COMMENTlink written 2.1 years ago by Guangchuang Yu1.1k

Great! It works! Thx!

ADD REPLYlink written 2.1 years ago by googneed0
0
gravatar for renuka.nayak
15 months 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?

ADD COMMENTlink written 15 months ago by renuka.nayak0

they are based on the ko database. If you want to use your own data, see http://guangchuangyu.github.io/2015/05/use-clusterprofiler-as-an-universal-enrichment-analysis-tool/.

ADD REPLYlink written 15 months ago by Guangchuang Yu1.1k
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