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Question: #clusterProfiler# KEGG enrichment with non-reference species
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gravatar for googneed
22 months 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 12 months ago by renuka.nayak0 • written 22 months ago by googneed0
2
gravatar for Guangchuang Yu
22 months ago by
Guangchuang Yu1.0k
Hong Kong
Guangchuang Yu1.0k wrote:

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

ADD COMMENTlink written 22 months ago by Guangchuang Yu1.0k

Great! It works! Thx!

ADD REPLYlink written 22 months ago by googneed0
0
gravatar for renuka.nayak
12 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 12 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 12 months ago by Guangchuang Yu1.0k
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