cpgDensityPlot: Plot the distribution of sequencing reads CpG densities.

Description Usage Arguments Details Value Author(s) Examples

Description

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

Usage

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  ## 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

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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)
}

Repitools documentation built on Nov. 17, 2017, 12:46 p.m.