segmentPMDs {MethylSeekR} | R Documentation |
This function trains a Hidden Markov Model (HMM) to detect partially methylated domains (PMDs) in Bis-seq data.
segmentPMDs(m, chr.sel, pdfFilename = NULL, seqLengths, num.cores = 1, nCGbin = 101)
m |
GRanges object containing the methylation data. |
chr.sel |
Chromosome on which HMM should be trained. 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. |
seqLengths |
A named vector indicating the chromosome lengths of the genome used. |
num.cores |
The number of cores used for the calculations (default 1). |
nCGbin |
The number of CpGs in each sliding window used to calculate alpha (default 101). The default is highly recommended. |
A GRanges object containing segments that partition the genome into PMDs and regions outside of PMDs. The object contains two metadata columns indicating the type of region (PMD/notPMD) and the number of covered (by at least 5 reads) CpGs (nCG) in the region. The function also creates a figure showing the inferred emission distributions of the HMM that is either printed to the screen (default) or saved as a pdf if a filename is provided.
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)