fragments_to_windows: Convert a list of GenomicRanges objects to a list of genomic...

In AllenInstitute/lowcat: Low Coverage Accessibility and Transcriptomics

Description

This function converts genomic positions to integer window positions based on the 5' end of each GenomicRanges region.

Usage

fragments_to_windows(fragment_list, window_size = 10000,
  collapse = TRUE)

Arguments

fragment_list	The list object containing GenomicRanges objects
window_size	The size of the genomic windows to use. Default is 1e4.
collapse	Logical to determine if fragments found in the same window should be merged after conversion. Default is TRUE.

Value

A nested list object. Each sample in the fragment list will result in a list containing vectors with integer values for windows on each chromosome.

AllenInstitute/lowcat documentation built on Oct. 30, 2019, 4:45 a.m.