calculate_relative_overlap1d: Relative Anchor Overlap of two Peaks

In kkrismer/idr2d: Irreproducible Discovery Rate for Genomic Interactions Data

Relative Anchor Overlap of two Peaks

Description

Calculates the overlap between anchor A of interaction 1 and anchor A of interaction 2, as well as anchor B of interaction 1 and anchor B of interaction 2. The overlap (in nucleotides) is then normalized by the length of the anchors.

Usage

calculate_relative_overlap1d(peak1_start, peak1_end, peak2_start, peak2_end)

Arguments

peak1_start	integer vector; genomic start coordinate(s) of peak in replicate 1
peak1_end	integer vector; genomic end coordinate(s) of peak in replicate 1
peak2_start	integer vector; genomic start coordinate(s) of peak in replicate 2
peak2_end	integer vector; genomic end coordinate(s) of peak in replicate 2

Value

numeric vector; relative overlaps between peak pairs

Examples

# 100% overlap
calculate_relative_overlap1d(100, 120,
                         100, 120)

# 50% overlap
calculate_relative_overlap1d(100, 120,
                         100, 110)

# negative overlap
calculate_relative_overlap1d(100, 120,
                         130, 140)

# larger negative overlap
calculate_relative_overlap1d(100, 120,
                         200, 220)

# vectorized example
calculate_relative_overlap1d(c(100, 100, 100, 100),
                         c(120, 120, 120, 120),
                         c(100, 100, 130, 200),
                         c(120, 110, 140, 220))

kkrismer/idr2d documentation built on Feb. 7, 2024, 2:23 p.m.