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