Find overlaps with ENCODE blacklists — find_blacklist

Identify peaks in the data which overlap (or are adjacent to?) regions blacklisted by ENCODE as having universally high DNAse HS or ChIP signal (basically mapping artifacts) See https://doi.org/10.1038/s41598-019-45839-z for more details

Usage

find_blacklist_overlaps(
  atac = NULL,
  peaks = NULL,
  genome = NULL,
  max_dist_to_blacklist_region = 0,
  blacklist_name = "ENCODE.blacklist"
)

Arguments

atac: (optional) an ScPeaks or McPeaks object
peaks: (optional) the intervals set to check
genome: (optional, required if checking peaks directly) the genome of the peaks
max_dist_to_blacklist_region: (optional) distance to nearest blacklist region which still qualifies for being blacklisted
blacklist_name: name of the blacklist intervals to use (default: "ENCODE.blacklist")

Value

blacklist_overlaps - a PeakIntervals object with peaks identified as overlapping blacklisted regions

Examples

if (FALSE) {
blacklist_overlaps <- find_blacklist_overlaps(atac = my_atac_mc, max_dist_to_blacklist_region = 100)
blacklist_overlaps <- find_blacklist_overlaps(peaks = my_peak_set, genome = "mm10")
}