cpgDensityPlot: Plot the distribution of sequencing reads CpG densities.

In markrobinsonuzh/Repitools: Epigenomic tools

Plot the distribution of sequencing reads CpG densities.

Description

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

Usage

  ## 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, ...)

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.

Details

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

Value

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

Author(s)

Aaron Statham

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)
}

markrobinsonuzh/Repitools documentation built on March 20, 2024, 6:04 a.m.