Open zxy0912 opened 2 months ago
conduct the DO analysis with DOSE::enrichDO(), problem with loading DOLite dataset.
library(clusterProfiler) library(org.Hs.eg.db) library(enrichplot) library(GOSemSim) library(DOSE) runDO <- function(gene_set, maxGSSize = 500) { eg <- bitr(gene_set, fromType = "SYMBOL", toType = "ENTREZID", OrgDb = "org.Hs.eg.db") edo_res <- enrichDO(gene = eg$ENTREZID, # OrgDb =org.Hs.eg.db, ont = "DOLite", pAdjustMethod = "BH", minGSSize = 10, maxGSSize = maxGSSize, pvalueCutoff = 1, qvalueCutoff = 0.2, readable = TRUE) return(edo_res) }
first time is OK
> edo_res <- runDO(genelist) 'select()' returned 1:1 mapping between keys and columns
failed when re-run the function
> edo_res <- runDO(genelist) 'select()' returned 1:1 mapping between keys and columns Error in get("DOLite2EG") : object 'DOLite2EG' not found
This issue can be fixed after reloading the DOSE package.
> detach("package:DOSE") > library(DOSE)
DOLite was removed in the current version.
conduct the DO analysis with DOSE::enrichDO(), problem with loading DOLite dataset.
first time is OK
failed when re-run the function
This issue can be fixed after reloading the DOSE package.