cpgDensityPlot: Plot the distribution of sequencing reads CpG densities.
In Repitools: Epigenomic tools

Description Usage Arguments Details Value Author(s) Examples

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

1 2	## S4 method for signature 'GRangesList' cpgDensityPlot(x, cols=rainbow(length(x)), xlim=c(0,20), lty = 1, lwd = 1, main="CpG Density Plot", verbose=TRUE, ...)

`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.

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

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

Aaron Statham

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)
}