Question: Adding geneset to missMethyl
0
gravatar for solveigbrunstad
6 months ago by
solveigbrunstad0 wrote:

Hello,

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:

    [ [1] ] $REACTOME_OPSINS
    [1] "10692"    "62764"    "38384"   "34843"    "848312"
    
    [ [1] ] $REACTOME_POL_SWITCHING
    [1] "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!

snp sequence gene • 180 views
ADD COMMENTlink written 6 months ago by solveigbrunstad0
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