cpgDensityPlot {Repitools} | R Documentation

## 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)
    }

[Package Repitools version 1.38.0 Index]