homeology.event: homeology.event

In mskilab/GxG: GxG: Genomic matrices and pairwise genomic features based on GenomicRanges and data.table

homeology.event

Description

homeology.event

Usage

homeology.event(
  event,
  pad = 100,
  thresh = 2,
  stride = 1,
  pad2 = 5,
  flip = FALSE,
  mc.cores = 1,
  anchor = TRUE,
  deanchor_gm = TRUE,
  mat = FALSE,
  genome = "~/DB/GATK/human_g1k_v37.fasta",
  bidirected_search = TRUE
)

Arguments

event	data.table of junctions
pad	width around junction breakpoint around which to search for homeology
thresh	string distance threshold for calling homeology in a bin
stride	distance in bases between consecutive bins in which we will be measuring homeology
pad2	number of bases of padding around each sequence position (bin) to use when computing homeology
flip	if flip = FALSE, homeology search for -/- and +/+ junctions is done between a sequence and its reverse complement
mc.cores	number of cores to use
anchor	if TRUE, anchor the junctions to the genome
deanchor_gm	if TRUE, deanchor the gMatrix
mat	if TRUE, return the gMatrix as a matrix
genome	path to .fasta containing genome sequence
bidirected_search	if TRUE, add padding on both sides of each breakpoint, if FALSE, add padding only in the direction of the fused side

mskilab/GxG documentation built on April 12, 2025, 5:32 p.m.