gpatterns.get_bg_meth: Get background trend expected methylation signal

In tanaylab/gpatterns: Single Molecule Methylation Patterns Analysis Suite

Get background trend expected methylation signal

Description

Calculate the expected average methylation given the background (CpG content driven) trend.

Usage

gpatterns.get_bg_meth(
  intervals,
  tracks = NULL,
  trend = NULL,
  cg_cont_track = .gpatterns.cg_cont_500_track,
  cg_cont_breaks = seq(0, 0.15, by = 0.002),
  ...
)

Arguments

intervals	genomic scope for which the function is applied
tracks	gpatterns tracks
trend	pre-computed global methylation trend (output of gpatterns.global_meth_trend).
cg_cont_track	CpG content track
cg_cont_breaks	breaks to determine the bins of cg_cont_track
...	Arguments passed on to gpatterns.global_meth_trend strat_track track to stratify average methylation by. default is CG content strat_breaks breaks to determine the bins of strat_track 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

intervals set with the additional fields 'exp_meth' 'exp_cov' and 'exp_avg' with the expected methylation calls, coverage and average methylation (respectively)

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