calculate_midpoint_distance2d: Distance between Anchor Midpoints of two Interactions

In idr2d: Irreproducible Discovery Rate for Genomic Interactions Data

Description

Calculates the distance in nucleotides between the anchor midpoints of two interactions, which is the sum of the distance between midpoints of anchor A in interaction 1 and anchor A in interaction 2, and the distance between midpoints of anchor B in interaction 1 and anchor B in interaction 2.

Note: all anchors must be on the same chromosome; start coordinate is always less than end coordinate

Usage

calculate_midpoint_distance2d(
  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

positive integer vector; distances between interaction pairs

Examples

# identical, zero distance
calculate_midpoint_distance2d(100, 120, 240, 260,
                              100, 120, 240, 260)

# centered, zero distance
calculate_midpoint_distance2d(100, 120, 240, 260,
                              90, 130, 230, 270)

# off by 10 per anchor
calculate_midpoint_distance2d(100, 120, 240, 250,
                              110, 130, 230, 240)

# off by 10 (anchor B only)
calculate_midpoint_distance2d(100, 120, 240, 250,
                              90, 130, 250, 260)

# vectorized example
calculate_midpoint_distance2d(c(100, 100, 100, 100),
                              c(120, 120, 120, 120),
                              c(240, 240, 240, 240),
                              c(260, 260, 250, 250),
                              c(100, 90, 110, 90),
                              c(120, 130, 130, 130),
                              c(240, 230, 230, 250),
                              c(260, 270, 240, 260))

idr2d documentation built on Nov. 8, 2020, 6:16 p.m.