simplifyEnrichment
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Published
20 hours ago •
jokergoo
jokergoo
Error message when running simplifyEnrichment function with clusterProfiler::GSEA() output
Hi. I'm trying to run simplifyEnrichment with enriched pathways from clusterProfiler GSEA function, but it gives me an error message. Below is an example with a similar analysis and the same error. I tried to provide the term names or descriptions by the term argument, but it didn't work.
suppressPackageStartupMessages(library(dplyr))
suppressPackageStartupMessages(library(msigdbr))
suppressPackageStartupMessages(library(clusterProfiler))
suppressPackageStartupMessages(library(simplifyEnrichment))
data(geneList, package="DOSE")
C2reactome_t2g <- msigdbr(species = "Homo sapiens", category = "C2",
subcategory = "REACTOME") %>%
select(gs_name, entrez_gene)
em2 <- GSEA(geneList, TERM2GENE = C2reactome_t2g, eps = 0)
#> preparing geneSet collections...
#> GSEA analysis...
#> leading edge analysis...
#> done...
mat <- term_similarity_from_enrichResult(em2)
mat.clust <- simplifyEnrichment(mat)
#> Cluster 264 terms by 'binary_cut'...
#> 51 clusters, used 0.6444671 secs.
#> Error in .local(object, ...): unused argument (term = NULL)
Created on 2022-10-19 with reprex v2.0.2
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
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#> date 2022-10-19
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#>
#> ──────────────────────────────────────────────────────────────────────────────
Very old issue at this point, but for others encountering this error with custom gene sets, I precluded it by supplying the argument plot = FALSE to simplifyEnrichment()
