averageMethylationRegions: Computes and plots the average distribution of aligned reads...

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

Description

Given an alignmentData or alignmentMeth object and a set of coordinates, plots the average distribution of coverage/methylation over those coordinates. The plotted distributions can be split up into different sample groups by the user.

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.

Value

Invisibly, a list containing the coordinates of the lines plotted.

Author(s)

Thomas J. Hardcastle

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