Problems: CpG annotation

[dnalinkbi]

I was trying to annotate with 'CpG.Relation' data using RnBeads, but I ran into an unexpected problem.
Below is the code I used.

library(RnBeads)
library(RnBeads.hg38)
rnb.sites <- rnb.get.annotation(type = "CpG", assembly = "hg38")
rnb.sites.df <- as.data.frame(rnb.sites)
rnb.sites.df[rnb.sites.df$seqnames == "chr1" & rnb.sites.df$start >= 133000 & rnb.sites.df$end <= 133150, ]

Below is the result

group group_name seqnames start end width strand CpG GC CGI.Relation SNPs
2675 1 chr1 chr1 133000 133001 2 + 5 62 Open Sea
2676 1 chr1 chr1 133000 133001 2 - 5 62 Open Sea
2677 1 chr1 chr1 133031 133032 2 + 3 62 Open Sea
2678 1 chr1 chr1 133031 133032 2 - 3 62 Open Sea
2679 1 chr1 chr1 133033 133034 2 + 3 61 Open Sea
2680 1 chr1 chr1 133033 133034 2 - 3 61 Open Sea
2681 1 chr1 chr1 133145 133146 2 + 3 59 Shore
2682 1 chr1 chr1 133145 133146 2 - 3 59 Shore

'Open Sea' and 'Shore' should have a difference of at least 2kb, but it was strange that there was only a 112bp difference, so I checked other regions. And I found that information that should be marked as 'Shelf' or 'Shore' is marked as 'Open Sea'.

Please let me know if there is anything I have used incorrectly.

[schmic05]

Hi @dnalinkbi ,

Thanks for reporting the issue! We are currently working on a new annotation version of RnBeads and will also fix this issue then. For now, I would suggest that you use a custom CGI/shelf/shore/open sea annotation.