Repitools (version 1.18.0)

cpgDensityPlot: Plot the distribution of sequencing reads CpG densities.

Description

Function to generate a plot of the distribution of sequencing reads CpG densities.

Usage

"cpgDensityPlot"(x, cols=rainbow(length(x)), xlim=c(0,20), lty = 1, lwd = 1, main="CpG Density Plot", verbose=TRUE, ...)

Arguments

x

A GRangesList object of reads to plot CpG density of

cols

The line colour for each element of x

xlim

xlim parameter passed to plot.

lty

The line type for each element of x

lwd

The line width for each element of x

main

main parameter passed to plot

verbose

Print details of processing.

...

Arguments passed into cpgDensityCalc. seq.len and organism are required.

Value

A plot is created. The data processed by cpgDensityCalc is invisibly returned.

Details

See cpgDensityCalc for details of options for calculating the CpG density.

Examples

if(require(BSgenome.Hsapiens.UCSC.hg18))
{
  data(samplesList) # Loads 'samples.list.subset'.
  cpgDensityPlot(samples.list.subset, seq.len=300, organism=Hsapiens, lwd=4, verbose=TRUE)
}