makeWindowFragments: Make windows merging restriction fragments

In Pasquali-lab/UMI4Cats: UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

Make windows merging restriction fragments

Description

Use a set of continuous restriction fragments to generate windows containing a fixed number of fragments (n_frags).

Usage

makeWindowFragments(input, n_frags = 8, sliding = 1)

Arguments

input	Input object containing the restriction fragments. Should be class UMI4C (rowRanges will be extracted) or class GRanges.
n_frags	Number of fragments to use for generating the windows. This should include restriction fragments with 0 counts (Default: 8).
sliding	Numeric indicating the factor for generating sliding windows. If set to 1 (default) will use fixed windows. If set to > 0 and < 1 will use n_frags * sliding fragments to generate sliding windows.

Value

A GRanges object containing the windows of merged restriction fragments.

Examples

data("ex_ciita_umi4c")

# Without sliding windows
win_frags <- makeWindowFragments(ex_ciita_umi4c, n_frags=30, sliding=1)
win_frags

# With sliding windows (n_frags*sliding)
win_frags <- makeWindowFragments(ex_ciita_umi4c, n_frags=30, sliding=0.5)
win_frags

Pasquali-lab/UMI4Cats documentation built on Nov. 3, 2024, 3:10 p.m.