find_overlapping_ccans: Find CCANs that overlap each other in genomic coordinates

In cicero: Precict cis-co-accessibility from single-cell chromatin accessibility data

Description

Find CCANs that overlap each other in genomic coordinates

Usage

find_overlapping_ccans(ccan_assignments, min_overlap = 1)

Arguments

ccan_assignments	A data frame where the first column is the peak and the second is the CCAN assignment. For example, output of generate_ccans.
min_overlap	The minimum base pair overlap to count as overlapping.

Value

A data frame with two columns, CCAN1 and CCAN2. CCANs in this list are overlapping. The data frame is reciprocal (if CCAN 2 overlaps CCAN 1, there will be two rows, 1,2 and 2,1).

Examples

  ccan_df <- data.frame(peak = c("chr18_1408345_1408845", "chr18_1779830_1780330", 
                                 "chr18_1929095_1929595", "chr18_1954501_1954727",
                                 "chr18_2049865_2050884", "chr18_2083726_2084102",
                                 "chr18_2087935_2088622", "chr18_2104705_2105551",
                                 "chr18_2108641_2108907"), 
                        CCAN = c(1,2,2,2,3,3,3,3,2))
  olap_ccans <- find_overlapping_ccans(ccan_df)

cicero documentation built on Dec. 10, 2020, 2 a.m.