bpRegioneR: Run regioneR for to regions in bed format

In nriddiford/svBreaks: Analyse structrual variant breakpoint data as produced by [svParser](https://github.com/nriddiford/svParser)

Description

Run regioneR for to regions in bed format

Usage

bpRegioneR(
  ...,
  regionA = system.file("extdata", "notch_breakpoint_regions_500_mappable.bed", package
    = "svBreaks"),
  regionB = system.file("extdata", "motif_1.mappable.bed", package = "svBreaks"),
  mappable_regions = system.file("extdata", "dmel6_mappable.bed", package = "svBreaks"),
  chrom_lengths = system.file("extdata", "chrom.sizes.txt", package = "svBreaks"),
  slop,
  limit2chrom = TRUE,
  chrom = "X",
  from,
  to,
  n = 100,
  plot = TRUE,
  bins = "auto",
  region = NULL
)

Arguments

regionA	RegionA [Required]
regionB	RegionB [Required]
mappable_regions	Bed file with mappable geneome [Required]
chrom_lengths	Lengths for for chromosomes
slop	Add this much slop to each region
limit2chrom	Restrict permutaions to one chromsome [Default: TRUE]
chrom	Chromosome to run permutations on if limit2chrom=TRUE [Default: "X"]
from	Restrict to region between from and to
to	Restrict to region between from and to
n	Number of permutations to run
plot	Return plot or not? [Default: TRUE]
region	Limit to region (chr:start-stop) [Default: NULL]

nriddiford/svBreaks documentation built on Dec. 29, 2021, 5:10 p.m.