Usage
averageProfiles(mD, samples, coordinates, cuts, maxcuts = 200, bw =
5000, surrounding = 0, add = FALSE, col, ylim, meanOnly = TRUE, plot =
TRUE, ...)
plotAverageProfile(position, profiles, col, surrounding, ylim, add =
FALSE, meanOnly = TRUE, legend = TRUE, titles, ...)
Arguments
mD
The alignmentData or
alignmentMeth object defining the
coverage or methylation on the genome.
samples
A factor or list defining the different groups of samples for which
to plot different distributions. If a list, each member should
consist of integer values defining the column numbers of the 'mD'
object. If missing, will use the mD@replicates value.
coordinates
A GRanges object defining the coordinates of
interest (e.g. genic regions).
cuts
Optionally, the number of subdivisions to cut the coordinates in
when calculating the average coverage/methylation density.
maxcuts
The maximum number of subdivisions permitted when calculating the
average coverage/methylation density.
bw
If 'cuts' is missing, this factor divides the product of the length of the
'coordinates' object and the median width of the coordinates to
defines the number of cuts (minimum twenty cuts).
surrounding
If non-zero, the size of the region up- and down-stream of the given
coordinates for which average coverage/methylation should also be calculated.
add
If TRUE, the plotted distribution will be added to the current plot.
col
If given, a vector of colours for each of the groups defined in
'samples'. Defaults to 'rainbow(length(samples))'.
ylim
See `ylim' option for plot. If missing, will be calculated from
data.
meanOnly
If TRUE, the mean methylation profile for each member of the
'samples' parameter is plotted on a single graph. If FALSE, every
5th percentile is plotted for each member of the sample parameters,
each on a separate graph.
plot
Should the profile be plotted? Defaults to TRUE.
position
A vector describing the position of each point to be plotted. Take
from the `$position' element in the list object returned by
`averageProfiles'.
profiles
A matrix describing the profiles to be plotted. Take
from the `$profiles element in the list object returned by
`averageProfiles'.
legend
If TRUE, a legend describing the samples is included on the plot.
titles
If given, and `meanOnly = FALSE', a vector of titles for the
quantile plots.
...
Additional arguments to be passed to the 'plotAverageProfile'
function, and hence to the 'plot' or 'lines' methods.