find_overlapping_coordinates: Find peaks that overlap a specific genomic location

In cole-trapnell-lab/cicero: Predict cis-co-accessibility from single-cell chromatin accessibility data

Find peaks that overlap a specific genomic location

Description

Find peaks that overlap a specific genomic location

Usage

find_overlapping_coordinates(coord_list, coord, maxgap = 0)

Arguments

coord_list	A list of coordinates to be searched for overlap in the form chr_100_2000.
coord	The coordinates that you want to find in the form chr1_100_2000.
maxgap	The maximum distance in base pairs between coord and the coord_list that should count as overlapping. Default is 0.

Value

A character vector of the peaks that overlap coord.

Examples

  test_coords <- c("chr18_10025_10225", "chr18_10603_11103",
                   "chr18_11604_13986",
                   "chr18_157883_158536", "chr18_217477_218555",
                   "chr18_245734_246234")
  find_overlapping_coordinates(test_coords, "chr18:10,100-1246234")

cole-trapnell-lab/cicero documentation built on March 13, 2023, 6:02 p.m.