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

plotMeth {BiSeq}

R Documentation

Plots raw and smoothed methylation data for a given region

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

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)