plotMeth: Plots a map of cytosine methylation (and optionally,...

In segmentSeq: Methods for identifying small RNA loci from high-throughput sequencing data

Description

This function takes an alignmentMeth object and plots the observed levels of methylation within some defined region on the genome. If a methData object is also supplied, loci of methylation will also be shown.

Usage

plotMeth(aM, loci, chr, limits, samples, showNumber = TRUE, rgb = c(1, 0, 0), angle = 45, cap, add = FALSE)

Arguments

aM	An alignmentMeth.
loci
chr	The name of the chromosome to be plotted. Should correspond to a chromosome name in the alignmentMeth object.
limits	The start and end point of the region to be plotted.
samples	The sample numbers of the samples to be plotted. If NULL, plots all samples.
showNumber	Should the row number of each segment be shown?
rgb	The rgb code (rgb) with which to colour the loci.
angle	The angle at which loci are shaded (see rect).
cap	Caps the maximum level of coverage shown on the plot; thus, if a base has been sequenced at a level greater than the cap, the data for that base will be shown as if it has a coverage of cap.
add	If TRUE, adds the plot of methylation level to the current plot. Defaults to FALSE.

Value

Plotting function.

Author(s)

Thomas J. Hardcastle

See Also

alignmentMeth

segmentSeq documentation built on Nov. 8, 2020, 5:18 p.m.