homeology.wrapper: homeology.wrapper

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

homeology.wrapper

Description

homeology.wrapper

Usage

homeology.wrapper(
  junctions,
  width = 50,
  pad = 0,
  thresh = 0,
  stride = 0,
  genome = "~/DB/GATK/human_g1k_v37.fasta",
  cores,
  flip = FALSE,
  bidirectional = TRUE,
  annotate = TRUE,
  overwrite = FALSE,
  save = TRUE,
  outdir = "./"
)

Arguments

junctions	Path to .vcf or bedpe or rds file of junctions or gGraph from which alt edges will be taken
width	width around junction breakpoint around which to search for homeology
pad	number of bases of padding around each sequence position (bin) to use when computing homeology, i.e. we then will be comparing 1 + 2*pad -mer sequences for edit distance
thresh	string distance threshold for calling homeology in a bin
stride	distance in bases between consecutive bins in which we will be measuring homeology
genome	Path to .fasta containing genome sequence
cores	How many cores to use
flip	if flip = FALSE, homeology search for -/- and +/+ junctions is done between a sequence and its reverse complement
bidirectional	adding padding on both sides of each breakpoint (TRUE) or only in the direction of the fused side (FALSE)
annotate	annotate edges in gGraph object and save it in working directory
save	save intermediate files and gMatrix? (default = TRUE)
outdir	output directory

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