Error in GOmeth function of missMethyl when EPICv2 annotation is used
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Entering edit mode
s.malik • 0
@89fab1ac
Last seen 7 weeks ago
Pakistan

Hi, after performing this code

sigCpGs <- DMPs$Name[DMPs$adj.P.Val<0.05]
length(sigCpGs)
[1] 311082
all <- DMPs$Name
length(all)
[1] 870529
par(mfrow=c(1,1))
gst <- gometh(sig.cpg=sigCpGs, all.cpg=all, plot.bias=TRUE)

I got following error All input CpGs are used for testing. Error in getMappedEntrezIDs(sig.cpg = sig.cpg, all.cpg = all.cpg, array.type = array.type, : There are no genes annotated to the significant CpGs

or if I mention array.type = "EPICv2" then I get All input CpGs are used for testing. Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'grepl': $ operator is invalid for atomic vectors

or if I use minfi created object annEPICv2 <- getAnnotation(IlluminaHumanMethylationEPICv2anno.20a1.hg38) then error is All input CpGs are used for testing. Error in strsplit(ann.keep$UCSC_RefGene_Group, split = ";") : non-character argument

plz help resolve this issue.

R 4.3.2 x86_64-w64-mingw32 Bioconductor 3.18 missMethyl 1.36 minfi 1.48

DNAMethylation GO MethylationArray missMethyl EPICv2 • 300 views
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Entering edit mode
@belindaphipson-6783
Last seen 10 weeks ago
Australia

Hi, currently the gene set testing functionality in missMethyl doesn't support EPICv2. It's on the to-do list. Cheers, Belinda

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