averageProfiles {segmentSeq} | R Documentation

## Computes and plots the average distribution of aligned reads (taken from an alignmentData object) or methylation (taken from an alignmentMeth object) over a set of coordinates (and optionally the surrounding regions).

### 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

[Package segmentSeq version 2.21.0 Index]