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