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Question: #clusterProfiler# KEGG enrichment with non-reference species
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gravatar for googneed
14 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 4 months ago by renuka.nayak0 • written 14 months ago by googneed0
2
gravatar for Guangchuang Yu
14 months ago by
Hong Kong
Guangchuang Yu800 wrote:

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

ADD COMMENTlink written 14 months ago by Guangchuang Yu800

Great! It works! Thx!

ADD REPLYlink written 14 months ago by googneed0
0
gravatar for renuka.nayak
4 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 4 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 4 months ago by Guangchuang Yu800
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