refragment

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.