enrichmentPlot: Plot the distribution of sequencing enrichment.

In markrobinsonuzh/Repitools: Epigenomic tools

Plot the distribution of sequencing enrichment.

Description

Function to generate a plot of the distribution of sequencing reads enrichments.

Usage

  ## S4 method for signature 'GRangesList'
enrichmentPlot(x, seq.len, cols = rainbow(length(x)),
      xlim = c(0, 20), main = "Enrichment Plot", total.lib.size = TRUE, verbose = TRUE, ...)

Arguments

x	A GRangesList object of reads to plot enrichment of. The chromosome lengths must be stored in the Seqinfo of this object.
seq.len	The fragment size to be used for extending the sequencing reads.
cols	The line colour for each element of x
xlim	xlim parameter passed to plot, the default is appropriate for "linear" cpgDensityCalc weighting.
main	main parameter passed to plot
total.lib.size	Whether to normalise enrichment values to the total number of reads per lane.
verbose	Print details of processing.
...	Additional graphical parameters to pass to plot.

Details

See enrichmentCalc for details of how the results are determined.

Value

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

Author(s)

Aaron Statham

Examples

  data(samplesList)  # GRangesList of reads 'samples.list.subset'
  enrichmentPlot(samples.list.subset, seq.len = 300, total.lib.size = FALSE)

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