RnBeads (version 1.4.0)

rnb.plot.region.profile.density: rnb.plot.region.profiles

Description

Plots the density of methylation levels accross all regions of the specified type

Usage

rnb.plot.region.profile.density(rnb.set, sample, region.type = "", region.profile = NULL, extend.by = 0.33)

Arguments

rnb.set

RnBSet object

sample

Index or name of the sample for which the plot should be generated

region.type

Region type for which the plot should be generated

region.profile

Alternative to specifying region.type, the function can accept a region profile generated by the rnb.find.relative.site.coord function

extend.by

A number between 0 and 1 specifying the percentage by which a region is extended in order to capture methylation information before region start and after region end

Value

a ggplot2 object for plotting the plot shows the density of methylation levels of sites accross the specified region type for all regions of that type from 0 (region start) to 1 (region end). Sites in the flanking areas are also shown (coordinates <0 and="">1).

Examples

library(RnBeads.hg19)
data(small.example.object)
logger.start(fname=NA)
rnb.plot.region.profile.density(rnb.set.example,1,"genes")