intBed: Fetch integration sites from bed files

In Heath1210/intSiteR: Process fastq files to get precise integration site coordinates

Description

Combine bed files from alignment of merged and unmerged reads. Deduplication is based on UMI and breaking point as well as the relative duplicate degree of reads.

Usage

intBed(
  mgBed,
  fqBed,
  outdir = NULL,
  qThreshold = 20,
  theta = 100,
  fThreshold = 5,
  monoSite = 50,
  collapse = 7,
  mixBarcode = FALSE
)

Arguments

mgBed	the file path of bed from alignment of merged reads
fqBed	the file path of bed from alignment of unmerged reads
outdir	the folder of output
qThreshold	the threshold of alignment quality filter. Default value 20 means keep only > Q20.
theta	a parameter controlling the looseness of filter by duplicate degree
fThreshold	the minimum duplicate degree allowed for further analysis.
monoSite	a threshold that insiteCode with frequency above it will not be filtered by breaking point
collapse	whether neighboring sites collapsed to one.
mixBarcode	whether different samples with different barcode mixed in one library.

Heath1210/intSiteR documentation built on Dec. 17, 2021, 10:32 p.m.