plotCoverageSampleProfiles: Plots coverage profiles over a specific region

In M3D: Identifies differentially methylated regions across testing groups

Description

Plots the profile for each of the two testing groups. Within each group, the mean of methylation level is taken, smoothed and plotted, along with the individual values.

Usage

plotCoverageSampleProfiles(rrbs, CpGs, group1, group2, CpGindex,
  samples = NaN, plot_title = NaN)

Arguments

rrbs	An rrbs object containing methylation and coverage data as created using the BiSeq pacakge
CpGs	A GRanges object with each row being a testing region
group1	The name of the first testing group
group2	The name of the second testing group
CpGindex	The index within the CpGs object of the region we are plotting
samples	Names of specific samples in the groups to plot, defaults to all samples in both groups
plot_title	Optional title for the plot, overrides automatic title

Value

NULL, the function plots the profiles

Author(s)

Tom Mayo [e-mail]

Examples

# plot the 9th region in the Toy Data Set
data(rrbsDemo)
data(CpGsDemo)
plotMethProfile(rrbsDemo, CpGsDemo, 'H1-hESC', 'K562', 9)

M3D documentation built on April 29, 2020, 5:59 a.m.