bam_to_centres_bw: Write a bigwig file of Tn5 insertion depth

In SamBuckberry/RunATAC: Functions for Importing, Processing, Analyzing, Plotting and Reformatting ATAC-seq Data

Description

Write a bigwig file of Tn5 insertion depth

Usage

bam_to_centres_bw(bam_file, file, max_insert = 2000, nuc_range = c(189,
  247), scale_cpm = FALSE, ...)

Arguments

bam_file	Path to an ATAC-seq paired-end BAM file.
file	Path for output bigwig file. Extension should be .bw or .bigwig.
max_insert	The Maximum insert size for read fragments.
nuc_range	The nucleosome spaning fragment size range.
scale_cpm	Logical. Should the output be scaled to number of million mapped reads?
...	Arguments for readGAlignmentPairs.

Value

No object is returned. A file is written.

SamBuckberry/RunATAC documentation built on Aug. 2, 2021, 9:54 a.m.