RnBeads (version 1.4.0)

rnb.plot.region.profiles: rnb.plot.region.profiles

Description

Creates a composite plot showing the sample and groupwise smoothed estimates of methylation values accross all regions of the specified type

Usage

rnb.plot.region.profiles(rnb.set, group.index.list, region.type = "", region.profile = NULL, extend.by = 0.33, cvalues = rnb.getOption("colors.category"))

Arguments

rnb.set

RnBSet object

group.index.list

a list (preferably named) containing sample indices for each group a list of such lists is for instance generated by the rnb.sample.groups function.

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

cvalues

Color values that will be assigned to sample groups

Value

a ggplot2 object for plotting the plot shows the smoothed 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). Smoothing is stratified by sample (dashed lines) and sample group (thick solid lines). Cubic splines are used for smoothing

Examples

#Careful: this might take a while
library(RnBeads.hg19)
data(small.example.object)
logger.start(fname=NA)
rnb.plot.region.profiles(rnb.set.example,rnb.sample.groups(rnb.set.example)[[1]],"genes")