plotMeth: Plots raw and smoothed methylation data for a given region

In BiSeq: Processing and analyzing bisulfite sequencing data

Description

This function plots the raw and the smoothed methylation data for one sample and a given region. The smoothed data is shown as a line (one line per CpG cluster) and the raw data is shown as points with color intensities proportional to the coverage.

Usage

plotMeth(object.raw, object.rel, region, col.lines, lwd.lines, col.points, ...)

Arguments

object.raw	A BSraw with only one sample.
object.rel	A BSrel with only one sample.
region	A GRanges of length one.
col.lines	OPTIONAL. The color for the line representing the smoothed methylation values.
lwd.lines	OPTIONAL. The line width for the line representing the smoothed methylation values.
col.points	OPTIONAL. The color for the points representing the raw methylation levels.
...	Other graphical parameters passed to the plot function.

Author(s)

Katja Hebestreit

See Also

plotSmoothMeth, plot

Examples

data(rrbs)
data(predictedMeth)

region <- GRanges(seqnames="chr1", 
                  ranges=IRanges(start = 875200, 
                                 end = 875500))
plotMeth(object.raw = rrbs[,6],
         object.rel = predictedMeth[,6],
         region = region)

BiSeq documentation built on Nov. 8, 2020, 8:05 p.m.