bt.flank: Creates flanking interval(s) for each BED/GFF/VCF feature.

View source: R/bt.flank.R

bt.flankR Documentation

Creates flanking interval(s) for each BED/GFF/VCF feature.

Description

Creates flanking interval(s) for each BED/GFF/VCF feature.

Usage

bt.flank(
  i,
  g,
  b = NULL,
  l = NULL,
  r = NULL,
  s = NULL,
  pct = NULL,
  header = NULL,
  output = NULL
)

Arguments

i

<bed/gff/vcf>

g

<genome>

b

Create flanking interval(s) using -b base pairs in each direction. - (Integer) or (Float, e.g. 0.1) if used with -pct.

l

The number of base pairs that a flank should start from orig. start coordinate. - (Integer) or (Float, e.g. 0.1) if used with -pct.

r

The number of base pairs that a flank should end from orig. end coordinate. - (Integer) or (Float, e.g. 0.1) if used with -pct.

s

Define -l and -r based on strand. E.g. if used, -l 500 for a negative-stranded feature, it will start the flank 500 bp downstream. Default = false.

pct

Define -l and -r as a fraction of the feature's length. E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp "upstream". Default = false.

header

Print the header from the input 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.