rnb.plot.locus.profile: rnb.plot.locus.profile

In RnBeads: RnBeads

Description

Computes methylation distributions for various region types and sample groups

Usage

rnb.plot.locus.profile(
  rnbSet,
  chrom,
  start,
  end,
  grps = NULL,
  plot.m.regions = NULL,
  plot.m.heatmap = TRUE,
  plot.m.smooth = TRUE,
  cvals.grps = rnb.getOption("colors.category"),
  cvals.meth = rnb.getOption("colors.meth"),
  smooth.profile = "wide"
)

Arguments

rnbSet	RnBSet object
chrom	chromosome of window to plot
start	start coordinate of window to plot
end	end coordinate of window to plot
grps	a list of indices for each group to be compared or NULL if no sample grouping information should be displayed
plot.m.regions	character vector of region types whose methylation values should be displayed If grps is not NULL the methylation values will be separated by sample groups.
plot.m.heatmap	flag indicating whether sites methylation values should be displayed in a heatmap. If grps is not NULL the heatmaps will be separated by sample groups.
plot.m.smooth	flag indicating whether a scatterplot with smoothing curves should be displayed. If grps is not NULL the colors will be used to separate sample groups.
cvals.grps	colors to be used for the different groups
cvals.meth	colors to be used for methylation values and heatmaps
smooth.profile	profile to be used for the smoothing curves. Allowed values include wide (default) which yields smoother curvers and narrow which yields more "wiggly" curves

Value

a ggplot2 plot object containing the plot

Author(s)

Fabian Mueller

Examples

#see RnBeads vignette (section: 'Generating Locus Profile Plots') for examples

RnBeads documentation built on March 3, 2021, 2 a.m.