plotPMDSegmentation: Plotting the PMD Segmentation
In MethylSeekR: Segmentation of Bis-seq data

Description Usage Arguments Value Author(s) Examples

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

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

`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.

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.

Lukas Burger lukas.burger@fmi.ch

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)