bt.window: Examines a "window" around each feature in A and reports all...

In PhanstielLab/bedtoolsr: Bedtools Wrapper

Examines a "window" around each feature in A and reports all features in B that overlap the window. For each overlap the entire entry in A and B are reported.

Description

Examines a "window" around each feature in A and reports all features in B that overlap the window. For each overlap the entire entry in A and B are reported.

Usage

bt.window(
  a,
  b,
  abam = NULL,
  ubam = NULL,
  bed = NULL,
  w = NULL,
  l = NULL,
  r = NULL,
  sw = NULL,
  sm = NULL,
  Sm = NULL,
  u = NULL,
  c = NULL,
  v = NULL,
  header = NULL,
  output = NULL
)

Arguments

a	<bed/gff/vcf>
b	<bed/gff/vcf>
abam	The A input file is in BAM format. Output will be BAM as well. Replaces -a.
ubam	Write uncompressed BAM output. Default writes compressed BAM.
bed	When using BAM input (-abam), write output as BED. The default is to write output in BAM when using -abam.
w	Base pairs added upstream and downstream of each entry in A when searching for overlaps in B. - Creates symmetrical "windows" around A. - Default is 1000 bp. - (INTEGER)
l	Base pairs added upstream (left of) of each entry in A when searching for overlaps in B. - Allows one to define asymmetrical "windows". - Default is 1000 bp. - (INTEGER)
r	Base pairs added downstream (right of) of each entry in A when searching for overlaps in B. - Allows one to define asymmetrical "windows". - Default is 1000 bp. - (INTEGER)
sw	Define -l and -r based on strand. For example if used, -l 500 for a negative-stranded feature will add 500 bp downstream. - Default = disabled.
sm	Only report hits in B that overlap A on the _same_ strand. - By default, overlaps are reported without respect to strand.
Sm	Only report hits in B that overlap A on the _opposite_ strand. - By default, overlaps are reported without respect to strand.
u	Write the original A entry _once_ if _any_ overlaps found in B. - In other words, just report the fact >=1 hit was found.
c	For each entry in A, report the number of overlaps with B. - Reports 0 for A entries that have no overlap with B. - Overlaps restricted by -w, -l, and -r.
v	Only report those entries in A that have _no overlaps_ with B. - Similar to "grep -v."
header	Print the header from the A file prior to results.
output	Output filepath instead of returning output in R.

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