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sigven / oncoEnrichR

Explore the cancer relevance of your gene list
https://sigven.github.io/oncoEnrichR/
MIT License
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Column `RichFactor` doesn't exist #35

Closed mdozmorov closed 1 month ago

mdozmorov commented 1 month ago 
oeDB <- oncoEnrichR::load_db(cache_dir = file.path(dir_data, "oeDBcache"))
report_UP <- onco_enrich(query = c("OR4F5",  "OR4F29", "OR4F16", "AMY2A",  "AMY1A"), oeDB = oeDB)
...
INFO  [2024-09-12 09:55:27] MSIGdb/C2/CP:REACTOME - Enrichment/ORA clusterProfiler settings: Background geneset size = 20599
Error in `dplyr::rename()`:
! Can't rename columns that don't exist.
✖ Column `RichFactor` doesn't exist.

Happens with different gene lists. I regenerated oeDBcache, same error, persisted next day. Any workaround?

  1. The version of oncoEnrichR used: 1.5.2
sigven commented 1 month ago

Got it. Which version of clusterProfiler are you using?

I believe I noticed both RichFactor and FoldEnrichment as new output columns in the latest versions ofclusterProfiler::enrichGO, and clusterProfiler::enricher, hence the new code. I don't really use them (the variables), so I can comment them out, I believe.

Sorry for the mess-up.

mdozmorov commented 1 month ago

4.12.2. I just upgraded to 14.12.6, restarted R, the error is gone. Didn't know which package to update. Thank you!