Error with custom OrgDB: authorize alternative keytype

Question

Error with custom OrgDB: authorize alternative keytype

lassancejm opened this issue 4 years ago · comments

Thanks for taking the time to develop this package.

I am trying to use the package with my own OrgDb object, which I created using the function AnnotationForge::makeOrgPackage().

The issue I run into is that some of the called functions use 'ENTREZID' as keytype by default, while my OrgDb object was created using 'GID' to label gene IDs. Note that is imposed by the developer(s) of the AnnotationForge::makeOrgPackage function.

Error message below:

Error in testForValidKeytype(x, keytype): Invalid keytype: ENTREZID. Please use the keytypes method to see a listing of valid arguments.
Traceback:

1. reduceSimMatrix(simMatrix, scores, threshold = 0.7, orgdb = "org.Mybeast.eg.db")
2. getGoSize(rownames(simMatrix), orgdb)
3. suppressMessages(AnnotationDbi::select(orgdb, keytype = "ENTREZID", 
 .     columns = c("GO", "ONTOLOGY"), keys = AnnotationDbi::keys(orgdb, 
 .         keytype = "ENTREZID")))
4. withCallingHandlers(expr, message = function(c) if (inherits(c, 
 .     classes)) tryInvokeRestart("muffleMessage"))
5. AnnotationDbi::select(orgdb, keytype = "ENTREZID", columns = c("GO", 
 .     "ONTOLOGY"), keys = AnnotationDbi::keys(orgdb, keytype = "ENTREZID"))
6. AnnotationDbi::select(orgdb, keytype = "ENTREZID", columns = c("GO", 
 .     "ONTOLOGY"), keys = AnnotationDbi::keys(orgdb, keytype = "ENTREZID"))
7. .select(x, keys, columns, keytype, jointype = jointype, ...)
8. testSelectArgs(x, keys = keys, cols = cols, keytype = keytype, 
 .     fks = fks, skipValidKeysTest = skipValidKeysTest)
9. testForValidKeytype(x, keytype)
10. stop(msg)

I would be good to have the possibility to the specify the keytype when calling the functions.

ssayols · Answer 1 · Mon Nov 16 2020 21:27:07 GMT+0800 (China Standard Time)

good point. I just patched the version in Github so you can call the function to reduce the terms with a custom keytype, which defaults to ENTREZID:

     reduceSimMatrix(
       simMatrix,
       scores = NULL,
       threshold = 0.7,
       orgdb,
       keytype = "ENTREZID"
     )

Could you please install the latest version with devtools (devtools::install_github("https://github.com/ssayols/rrvgo")) and give it a go? I'll deploy the patch to Bioconductor but probably won't be available until tomorrow.

I don't have access to a custom orgdb object, so any feedback will be appreciated.
Thanks!

lassancejm · Answer 2 · Mon Nov 16 2020 21:46:42 GMT+0800 (China Standard Time)

I just ran a test with the latest github version and happy to report that it is working fine.

Thanks for your quick response!

ssayols · Answer 3 · Mon Nov 16 2020 21:55:50 GMT+0800 (China Standard Time)

excellent, thanks!

lassancejm · Answer 4 · Wed Jul 13 2022 22:08:51 GMT+0800 (China Standard Time)

I think this should be re-open. I had the same issue again today, using a version from Bioconductor (sorry can't tell which version) and had to revert back to installing from the github repo.

ssayols · Answer 5 · Wed Jul 13 2022 22:25:21 GMT+0800 (China Standard Time)

This should be fixed in rrvgo 1.4.4 (Bioconductor 3.13).
Could you confirm which version of rrvgo you have loaded, via sessionInfo()?

lassancejm · Answer 6 · Thu Jul 14 2022 19:06:00 GMT+0800 (China Standard Time)

Nvm, it seems that the issue is coming from the fact that I was using an older version of Bioconductor (3.12), so am limited in which version of rrvgo I can install via bioconductor. Will stick to the devel version than.

ssayols · Answer 7 · Fri Jul 15 2022 15:45:45 GMT+0800 (China Standard Time)

Thanks for the feedback! I'd prefer not to backport the feature to previous versions, unless you tell me the devel version doesn't work anymore on Bioconductor 3.12

lassancejm · Answer 8 · Fri Jul 15 2022 15:48:17 GMT+0800 (China Standard Time)

I understand. The devel version works fine as far as I can tell.