I have met upon a problem using the missMethyl package, using the 'gsameth' function.
By using this function, I want to specify which genesets I want to include in my test (compared to the 'gometh' function that only test in GO- and KEGG pathways). It is necessary that the genelist have Entrez Gene IDs for each gene. From the Broads Molecular Signatures Database, I have downloaded what I want to use as my genelist. It is the C2 curated gene set (.rdata file) (from here)
What I have tried to run in R is the following:
gsa <- gsameth(sig.cpg = sigCpGs, all.cpg = rownames(top), collection = genesets) topGSA(gsa)
genesets: curated gene set, an excerpt from the list looks like this:
[  ] $REACTOME_OPSINS  "10692" "62764" "38384" "34843" "848312" [  ] $REACTOME_POL_SWITCHING  "1483" "34345" "05948"
The error message I got is: "Error in collection [ [ i ] ] : subscript out of bounds" Is the problem that there are not any levels in the genelist? What will levels mean in this context?
How can I solve this? Thank you!