plotPMDSegmentation {MethylSeekR} | R Documentation

## Plotting the PMD Segmentation

### Description

This function generates a figure showing the PMD segmentation in a randomly chosen region.

### Usage

    plotPMDSegmentation(m, segs, numRegions = 1, pdfFilename=NULL, minCover = 5)

### Arguments

`m` | GRanges object containing the methylation data.
`segs` | GRanges object containing the PMD segmentation. Return value of the segmentPMDs function (see example).
`numRegions` | The number of randomly chosen regions to be plotted. The default (1) can only be changed if a pdfFilename is provided (see below).
`pdfFilename` | Name of the pdf file in which the figure is saved. If no name is provided (default), the figure is printed to the screen.
`minCover` | Only CpGs with a coverage of at least minCover reads will be used for plotting.

### Value

No return value. The function creates a figure showing the inferred segmentation for a randomly chosen region. The figure is either printed to the screen (default) or saved as a pdf if a filename is provided. If a filename (pdfFilename) is provided, several regions (set via the numRegions argument) can be plotted and saved in a multi-page pdf file. The randomly chosen region that is displayed is broken up into 6 panels and in each panel, the raw (ie unsmoothed) methylation levels of all CpGs with a minimal coverage of 5 reads are shown. PMDs are indicated as green bars, extending over the entire PMD.

### Author(s)

Lukas Burger lukas.burger@fmi.ch

### Examples

    library(MethylSeekR)

    # get chromosome lengths
    library("BSgenome.Hsapiens.UCSC.hg18")
    sLengths=seqlengths(Hsapiens)

    # read methylation data
    methFname <- system.file("extdata", "Lister2009_imr90_hg18_chr22.tab",
    package="MethylSeekR")
    meth.gr <- readMethylome(FileName=methFname, seqLengths=sLengths)

    #segment PMDs
    PMDsegments.gr <- segmentPMDs(m=meth.gr, chr.sel="chr22", seqLengths=sLengths)

    #plot PMD segmentation examples
    plotPMDSegmentation(m=meth.gr, segs=PMDsegments.gr, numRegions=1)

[Package MethylSeekR version 1.26.0 Index]