MethylSeekR (version 1.12.0)

plotAlphaDistributionOneChr: Calculate and plot alpha distribution.

Description

This function calculates the alpha values for a selected chromosome and plots the distribution of alpha values. The shape of the distribution is indicative of the presence or absence of partially methylated domains (PMDs).

Usage

plotAlphaDistributionOneChr(m, chr.sel, pdfFilename = NULL, num.cores = 1, nCGbin = 101)

Arguments

m

Methylation GRanges object.

chr.sel

Selected chromosome for which alpha values are calculated. Must be one of the sequence levels of m.

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.

num.cores

The number of cores that are used for the calculation (default 1).

nCGbin

The number of CpGs in each sliding window used to calculate alpha (default 101). The default is highly recommended.

Value

No return value. The function creates a figure showing the alpha distribution for the selected chromosome that is either printed to the screen (default) or saved as a pdf if a filename is provided.

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)

#calculate alpha distribution for one chromosome
plotAlphaDistributionOneChr(m=meth.gr, chr.sel="chr22", num.cores=1)