plot_fragments_length: Plot DNA fragment length distribution

In TearsWillFall/DNAfrags: Filter DNA fragments in BAM files by length and location

Plot DNA fragment length distribution

Description

This function takes a file with the fragment length as input and plots the length distribution of DNA fragments. The input file must not have headers and must contain the length of a single fragment per line.

Usage

plot_fragments_length(
  file = "",
  verbose = FALSE,
  min_frag_length = 2,
  max_frag_length = "",
  deviations = 10,
  width_span = 3,
  min_frgl_maximum = 2,
  min_maximum_distance = 10,
  max_maximum_distance = 11,
  vline = ""
)

Arguments

file	Path to file with fragment length.
verbose	Enables progress messages. Default False.
min_frag_length	Minimum fragment length to plot. Default 2.
max_frag_length	Max fragment length to plot. When not provided it uses the rounded value of MEDIAN + DEVIATIONS*MEDIAN ABSOLUTE DEVIATION as cut point.
deviations	MEDIAN + DEVIATIONS*MEDIAN ABSOLUTE DEVIATION. Default 10
width_span	Window of width span at which a peak is greater than all other elements around it. Default 3
min_frgl_maximum	Minimum fragment length at which to plot maximums peaks. Default 2
min_maximum_distance	Minimum distance between local maximum peaks to plot. Default 10
max_maximum_distance	Maximum distance between local maximum peaks to plot. Default 12
vline	Fragment length where to draw a vertical line. Default none

TearsWillFall/DNAfrags documentation built on March 26, 2022, 6:02 a.m.