refragment: refragment

In ETHZ-INS/epiwraps: epiwraps: Wrappers for plotting and dealing with epigenomics data

refragment

Description

Uses the cut profiles to re-fragment in silico fragments that contain more than a nucleosome.

Usage

refragment(
  bam,
  minSize = 20L,
  nfr = 120L,
  nuc = c(145, 190),
  binSize = 10L,
  verbose = TRUE,
  BPPARAM = BiocParallel::SerialParam()
)

Arguments

bam	Path to a paired-end bam file, or a 'GRanges' of fragments.
minSize	Minimum fragment size
nfr	Maximum size of nucleosome-free fragments
nuc	Range (min & max) of mono-nucleosome fragment sizes
binSize	Bin size for cut profile
verbose	Logical; whether to print progress messages
BPPARAM	'BiocParallel' param for multithreading.

Value

A list of processed fragment 'GRanges', including nucleosome-free, mono-nucleosome, and ambiguous fragments.

ETHZ-INS/epiwraps documentation built on May 4, 2024, 6:25 a.m.