diff --git a/CpG_annotations.R b/CpG_annotations.R new file mode 100644 index 0000000000000000000000000000000000000000..860f335822ecd62d02a7d7f1a837598d9b79018f --- /dev/null +++ b/CpG_annotations.R @@ -0,0 +1,17 @@ +library(BSgenome.Ggallus.UCSC.galGal6) +library(AnnotationHub) + +# all CpG sites --------- +# https://support.bioconductor.org/p/95239/ +chrs <- names(Ggallus)[c(1:32, 34, 35)] # chr1-33, chrW, chrZ +cgs <- lapply(chrs, function(x) start(matchPattern("CG", Ggallus[[x]]))) +cgs <- do.call(c, lapply(seq_along(chrs), function(x) GRanges(chrs[x], IRanges(cgs[[x]], width = 2)))) + +# CpG islands ---------- +# https://support.bioconductor.org/p/95239/ +hub <- AnnotationHub() +query(hub, c("cpg","gal")) +cgi <- hub[["AH7135"]] + +cgis <- intersect(cgs, cgi) +