CpG coordinates on a chromosome — find

For a given chromosome, returns positions of all "CG" dinucleotides (CpG sites) based on a human genome assembly hg19. If minimum or maximum position is given, only CpGs in the given range are returned.

find_CpG(chromosome, min_coord = NULL, max_coord = NULL)

Arguments

chromosome	Name of a human chromosome in the format `"chr?"`, where `"?"` must either be a number from `1` to `22` or `"X"` or `"Y"`.
min_coord	Minimum returned coordinate.
max_coord	Maximum returned coordinate.

Value

Vector of CpG coordinates.

Details

Returned position is a position of "C". The same convention is used by Illumina Infinium HM450K manifest file. Function is based on R package `"BSgenome.Hsapiens.UCSC.hg19"` (TBD 2020) .

References

TBD T (2020). BSgenome.Hsapiens.UCSC.hg19: Full genome sequences for Homo sapiens (UCSC version hg19, based on GRCh37.p13). R package version 1.4.3.