calculate_relative_overlap2d {idr2d} | R Documentation

## Relative Anchor Overlap of two Interactions

### 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.

Note: anchors A and B of the same interaction have to be on the same chromosome; start coordinate is always less than end coordinate

### Usage

    calculate_relative_overlap2d(
      int1_anchor_a_start,
      int1_anchor_a_end,
      int1_anchor_b_start,
      int1_anchor_b_end,
      int2_anchor_a_start,
      int2_anchor_a_end,
      int2_anchor_b_start,
      int2_anchor_b_end
    )

### Arguments

`int1_anchor_a_start` | integer vector; genomic start coordinate(s) of anchor A in replicate 1 interaction
`int1_anchor_a_end` | integer vector; genomic end coordinate(s) of anchor A in replicate 1 interaction
`int1_anchor_b_start` | integer vector; genomic start coordinate(s) of anchor B in replicate 1 interaction
`int1_anchor_b_end` | integer vector; genomic end coordinate(s) of anchor B in replicate 1 interaction
`int2_anchor_a_start` | integer vector; genomic start coordinate(s) of anchor A in replicate 2 interaction
`int2_anchor_a_end` | integer vector; genomic end coordinate(s) of anchor A in replicate 2 interaction
`int2_anchor_b_start` | integer vector; genomic start coordinate(s) of anchor B in replicate 2 interaction
`int2_anchor_b_end` | integer vector; genomic end coordinate(s) of anchor B in replicate 2 interaction

### Value

numeric vector; relative overlaps between interaction pairs

### Examples

    # 100% overlap
    calculate_relative_overlap2d(100, 120, 240, 260,
                                 100, 120, 240, 260)

    # 50% overlap
    calculate_relative_overlap2d(100, 120, 240, 250,
                                 100, 110, 240, 260)

    # negative overlap
    calculate_relative_overlap2d(100, 120, 240, 250,
                                 130, 140, 260, 280)

    # larger negative overlap
    calculate_relative_overlap2d(100, 120, 240, 250,
                                 200, 220, 340, 350)

    # vectorized example
    calculate_relative_overlap2d(c(100, 100, 100, 100),
                                 c(120, 120, 120, 120),
                                 c(240, 240, 240, 240),
                                 c(260, 250, 250, 250),
                                 c(100, 100, 130, 200),
                                 c(120, 110, 140, 220),
                                 c(240, 240, 260, 340),
                                 c(260, 260, 280, 350))

[Package idr2d version 1.1.4 Index]