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)
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.