bt.pairtopair: Report overlaps between two paired-end BED files (BEDPE).

In PhanstielLab/bedtoolsr: Bedtools Wrapper

Report overlaps between two paired-end BED files (BEDPE).

Description

Report overlaps between two paired-end BED files (BEDPE).

Usage

bt.pairtopair(
  a,
  b,
  f = NULL,
  type = NULL,
  slop = NULL,
  ss = NULL,
  is = NULL,
  rdn = NULL,
  output = NULL
)

Arguments

a	<BEDPE>
b	<BEDPE>
f	Minimum overlap required as fraction of A (e.g. 0.05). Default is 1E-9 (effectively 1bp).
type	Approach to reporting overlaps between A and B. neither Report overlaps if neither end of A overlaps B. either Report overlaps if either ends of A overlap B. both Report overlaps if both ends of A overlap B. notboth Report overlaps if one or neither of A's overlap B. - Default = both.
slop	The amount of slop (in b.p.). to be added to each footprint of A. *Note*: Slop is subtracted from start1 and start2 and added to end1 and end2. - Default = 0.
ss	Add slop based to each BEDPE footprint based on strand. - If strand is "+", slop is only added to the end coordinates. - If strand is "-", slop is only added to the start coordinates. - By default, slop is added in both directions.
is	Ignore strands when searching for overlaps. - By default, strands are enforced.
rdn	Require the hits to have different names (i.e. avoid self-hits). - By default, same names are allowed.
output	Output filepath instead of returning output in R.

PhanstielLab/bedtoolsr documentation built on Aug. 29, 2024, 5:37 p.m.