Question: Yeast org.Sc.sgd.db lacks SYMBOL - should it have one? - how to make it interoperate with clusterProfiler in its absence?
0
gravatar for Malcolm Cook
7 weeks ago by
Malcolm Cook1.5k
United States
Malcolm Cook1.5k wrote:

library org.Sc.sgd.db lacks a SYMBOL attribute and instead has COMMON and GENENAME

As a result, it does not interoperate with the clusterProfiler package when using the readable=TRUE option (without which genes are labelled by their ENTREZID, which is relatively uninformative).

clusterProfiler's author asserts:

this is the issue of org.Sc.sgd.db which doesn't contains SYMBOL while the GENENAME (expected full name that is descriptive and verbose) is actually the SYMBOL

Might org.Sc.sgd.db be changed to provide a SYMBOL?

In the mean time, is there a recommend best, quick, clever workaround (hack) to either:

  • modify the SQL backing store to use COMMON or GENENAME in place of SYMBOL
  • otherwise trick clusterProfiler into using COMMON or GENENAME instead of SYMBOL
ADD COMMENTlink modified 6 weeks ago • written 7 weeks ago by Malcolm Cook1.5k

You can always run the "non readable" test and then map the ids back to COMMON or GENENAME, this doesn't require modifying existing infrastructure

ADD REPLYlink written 7 weeks ago by Lluís Revilla Sancho460

Thanks, but...

I am able to run enrichGo(readable=FALSE, OrgDb=org.Sc.sgd.db, ...)

However, I would further like to use clusterProfiler::cnetplot and have the nodes labelled not with the ENTREZID which I understand requires me to have passed readable=TRUE.

I am looking for suggestions that can accomplish that, and I don't see how your suggestion does.

ADD REPLYlink written 7 weeks ago by Malcolm Cook1.5k

I was just answering how to obtain the "names" of the genes as it is your question, but your last comment is in another direction. That's why my comment doesn't help you with your plotting problems. After obtaining the "names" of the genes you can replace the internal data of the object to be used by cnetplot. Good luck

ADD REPLYlink written 7 weeks ago by Lluís Revilla Sancho460

I'd argue that

how to obtain the "names" of the genes

was not my original question at all.

But thanks for your original help. I posted my own "workaround" as a solution, below.

ADD REPLYlink written 6 weeks ago by Malcolm Cook1.5k
Answer: Yeast org.Sc.sgd.db lacks SYMBOL - should it have one? - how to make it interope
0
gravatar for Malcolm Cook
6 weeks ago by
Malcolm Cook1.5k
United States
Malcolm Cook1.5k wrote:

I found someone similarly afflicted who reported the issue as enrichPathway make readable does not work for yeast genome - this prompted further sleuthing on my part which resulted in more understanding and a workaround: "translate my ORFs to GENENAME (using bitr) and use them" as the keyType

ADD COMMENTlink written 6 weeks ago by Malcolm Cook1.5k
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