Entering edit mode
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
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
Thanks, but...
I am able to run
enrichGo(readable=FALSE, OrgDb=org.Sc.sgd.db, ...)However, I would further like to use
clusterProfiler::cnetplotand have the nodes labelled not with the ENTREZID which I understand requires me to have passedreadable=TRUE.I am looking for suggestions that can accomplish that, and I don't see how your suggestion does.
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 luckI'd argue that
was not my original question at all.
But thanks for your original help. I posted my own "workaround" as a solution, below.