We have used “GRCh37/hg19” for reference genome in our project. We convert output file to GenomicRange object that has been 3 columns included that: (Seqnames, ranges, strand).

We loud different packages about annotation for instance:

library("GenomicRanges")

library("AnnotationHub")

library("rtracklayer")

library(GenomicFeatures)

library(TxDb.Hsapiens.UCSC.hg19.knownGene)

Nowdays, we use “annotateDMRInfo(SigDMR,'TxDb.Hsapiens.UCSC.hg19.knownGene')”, but we encountered an error :

“annotateDMRInfo(SigDMR,'TxDb.Hsapiens.UCSC.hg19.knownGene')

Error in txName.known[naInd] <- names(tss)[nearestInfo.tr[, "subjectHits"]] :

replacement has length zero

In addition: Warning message: In .Seqinfo.mergexy(x, y) :

The 2 combined objects have no sequence levels in common. (Use

suppressWarnings() to suppress this warning.)”