Dear all, I have two Grnage list (gr2=repeatmask.hg38 from UCSC; gr1=CpGs methylation regions from RRBS data). I want to filter out the CpGs that are in the genome repeated regions. I did it like this, do you think if it is correct?

hits <- findOverlaps(gr2, gr1)

head(hits)

Hits object with 6 hits and 0 metadata columns:

queryHits subjectHits

<integer>   <integer>

[1] 2 11832

[2] 2 11833

[3] 2 11834

queryLength: 5520017 / subjectLength: 58660550

idx <- unique(subjectHits(hits))

head(idx)

[1] 11832 11833 11834 11835 11840 11841

rownames(gr1) <- gr1$ids

gr1_unique <- gr1[! ids %in% idx,]

OR

unique_gr1 <- gr1[-match(idx,gr1$ids),]

Many thnkas in advance, Rahel