Plot global methylation stratified on other tracks

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).

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')

Examples