gpatterns.global_meth_trend: Plot global methylation stratified on other tracks

In tanaylab/gpatterns: Single Molecule Methylation Patterns Analysis Suite

Plot global methylation stratified on other tracks

Description

calculates the average methylation (m / m + um) in each bin of strat_track and plots it. By default, plots the average methylation in different bins of CpG content. This can be used as a sanity check for methylation data - in general, methylation is high for regions with low CpG density, and low for CpG dense regions (e.g. CpG islands).

Usage

gpatterns.global_meth_trend(
  tracks,
  strat_track = .gpatterns.cg_cont_500_track,
  strat_breaks = seq(0, 0.08, by = 0.002),
  intervals = .gpatterns.genome_cpgs_intervals,
  iterator = .gpatterns.genome_cpgs_intervals,
  min_cov = NULL,
  min_cgs = NULL,
  names = NULL,
  groups = NULL,
  group_name = NULL,
  include.lowest = TRUE,
  ncol = 2,
  nrow = 2,
  width = 600,
  height = 560,
  fig_fn = NULL,
  xlab = strat_track,
  ylim = c(0, 1),
  title = "",
  legend = TRUE,
  colors = NULL,
  parallel = getOption("gpatterns.parallel")
)

Arguments

tracks	tracks to plot
strat_track	track to stratify average methylation by. default is CG content
strat_breaks	breaks to determine the bins of strat_track
intervals	genomic scope for which the function is applied
iterator	track expression iterator (of both tracks and strat_track)
min_cov	minimal coverage of each track
min_cgs	minimal number of CpGs per bin
names	alternative names for the track
groups	a vector the same length of tracks with group for each track. Each group will on a different facet.
group_name	name of the grouping variable (e.g. tumor, sample, patient, experiment)
include.lowest	if 'TRUE', the lowest value of the range determined by breaks is included
ncol	number of columns
nrow	number of rows
width	plot width (if fig_fn is not NULL)
height	plot height (if fig_fn is not NULL)
fig_fn	output filename for the figure (if NULL, figure would be returned)
xlab	label for the x axis
ylim	ylim of the plot
title	title for the plot
legend	add legend
colors	custom colors
parallel	get trends parallely

Value

list with trend data frame (under 'trend') and the plot (under 'p')

tanaylab/gpatterns documentation built on May 15, 2023, 6:23 p.m.