plotMethDistribution: Plots the distribution of methylation on the genome.
In segmentSeq: Methods for identifying small RNA loci from high-throughput sequencing data

Description Usage Arguments Details Value Author(s) See Also

View source: R/plotGenomicDistributions.R

Plots the distribution of methylation (as defined in an alignmentMeth object upon the genome.

1 2	plotMethDistribution(meth, samples, bw = 1e-3, subtract, chrs, centromeres, add = FALSE, col, ylim = NULL, legend = TRUE, ...)

`meth`	An object of class `alignmentMeth` containing the methylation data.
`samples`	A numeric vector defining the columns of data in the ‘meth’ object from which to estimate proportions of methylation, or a list object containing numeric vectors if multiple distributions are to be derived from the ‘meth’ object, or a factor in which each level of the factor defines a set of columns for the ‘meth’ object. If missing, derived from the ‘@replicates’ slot of the ‘meth’ object.
`bw`	Gives the bandwidth of the density plots; analagous to the ‘bw’ parameter in `density`.
`subtract`	A numeric vector giving values to be subtracted from the density of methylation. See Details.
`chrs`	The names of the chromosomes for which a distribution should be plotted. If mising, derived from the ‘@alignments’ slot of the ‘meth’ object.
`centromeres`	If given, a numeric vector defining the position of the centromeres on the chromosomes. These will be then be plotted.
`add`	Should the distribution curve be added to an existing plot? Defaults to FALSE.
`col`	A vector of colours to be used to plot the distributions. If missing, generated from `rainbow`.
`ylim`	Limits on the y-axis. Defaults to NULL, in which case limits are automatically set.
`legend`	Should a legend be added to the plot? Defaults to TRUE.
`...`	Any additional parameters to be passed to `plot`.

The function returns the density of methylation calculated. This can be used in further plots as the 'subtract' parameter, which allows one methylation profile to be subtracted from another.

An object of class density describing the plotted distribution.

Thomas J. Hardcastle

alignmentMeth

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