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error running in example code

Open sumin5784 opened this issue 6 days ago • 4 comments

Describe the bug I installed the package and ran the example code in document, and I got this error. I tried with other query gene sets but the error was the same.

INFO  [2025-02-20 13:14:18] WARNING: target gene identifiers NOT found as primary symbols: CCDC101, SMEK1, MGEA5, DGCR14
INFO  [2025-02-20 13:14:18] Trying to map target gene identifiers as gene aliases/synonyms: CCDC101, SMEK1, MGEA5, DGCR14
INFO  [2025-02-20 13:14:18] Mapped query identifiers as gene aliases CCDC101, SMEK1, MGEA5, DGCR14 ---> SGF29, PPP4R3A, OGA, ESS2
INFO  [2025-02-20 13:14:18] SUCCESS: Identified all genes (n = 134) in target set
INFO  [2025-02-20 13:14:18] Open Targets Platform: annotation of protein targets to disease phenotypes (minimum association score =  0.05)
INFO  [2025-02-20 13:14:18] Open Targets Platform: annotation of protein targets to targeted drugs (cancer indications only)
INFO  [2025-02-20 13:14:18] Open Targets Platform: annotation of target tractabilities (druggability)
INFO  [2025-02-20 13:14:18] MSIGdb/H/ALL - Enrichment/ORA: performing gene enrichment analysis of target set with clusterProfiler
INFO  [2025-02-20 13:14:18] MSIGdb/H/ALL - Enrichment/ORA clusterProfiler settings: p_value_cutoff = 0.05, q_value_cutoff = 0.2
INFO  [2025-02-20 13:14:18] MSIGdb/H/ALL - Enrichment/ORA clusterProfiler settings: p_value_adjustment_method = BH
INFO  [2025-02-20 13:14:18] MSIGdb/H/ALL - Enrichment/ORA clusterProfiler settings: minGSSize = 10
INFO  [2025-02-20 13:14:18] MSIGdb/H/ALL - Enrichment/ORA clusterProfiler settings: maxGSSize = 500
INFO  [2025-02-20 13:14:18] MSIGdb/H/ALL - Enrichment/ORA clusterProfiler settings: Background geneset: 'All protein-coding genes'
INFO  [2025-02-20 13:14:18] MSIGdb/H/ALL - Enrichment/ORA clusterProfiler settings: Background geneset size = 20599
Error in `dplyr::rename()`:
! Can't rename columns that don't exist.
x Column `RichFactor` doesn't exist.
Run `rlang::last_trace()` to see where the error occurred.
  1. The version of oncoEnrichR used: oncoEnrichR_1.5.2
  2. The queryset used (gene identifiers): I ran example code in document
  3. The complete set options (explicitly) set when running oncoEnrichR: I ran example code in document (see below)
library(oncoEnrichR)
myc_interact_targets <- read.csv(system.file("extdata","myc_data.csv", package = "oncoEnrichR"), stringsAsFactors = F)
oeDB <- oncoEnrichR::load_db(cache_dir = "<LOCAL_FOLDER>")
myc_report <- oncoEnrichR::onco_enrich(
  query = myc_interact_targets$symbol, 
  oeDB = oeDB, 
  project_title = "cMYC BioID screen", 
  project_owner = "Raught et al."
  )
oncoEnrichR::write(report = myc_report, oeDB = oeDB, file = "<LOCAL_FOLDER>/myc_report_oncoenrichr.html", format = "html")
oncoEnrichR::write(report = myc_report, oeDB = oeDB, file = "<LOCAL_FOLDER>/myc_report_oncoenrichr.xlsx", format = "excel")

I didn't have this error with galaxy, I don't know why. Could you please check this? I want to R package instead using galaxy.

Thanks, Sumin

sumin5784 avatar Feb 20 '25 18:02 sumin5784