makeWindowFragments {UMI4Cats} | R Documentation

## 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

[Package UMI4Cats version 1.2.1 Index]