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
missMethyl has now been updated to support the EPICv2 array for the BioC 3.20 release. To access the functionality now please install the development version of missMethyl.
thanks, will give it a try