findPMDs {methylPipe} | R Documentation

## Identifying Partially Methylated Domains (PMDs)

### Description

This function is a wrapper function to identify partially methylated domains (PMDs) in Bis-seq data.

### Usage

    ## S4 method for signature 'methylPipe,BSdata'
    findPMDs(Object, Nproc=1, Chrs=NULL)

### Arguments

`Object` | An object of class BSdataSet
`Nproc` | numeric; the number of processors to use, one chromosome is ran for each processor
`Chrs` | character; Chromosome on which PMDs are identified

### Details

This functions is a wrapper function of segmentPMDs method of package MethylSeekR. This function trains a Hidden Markov Model (HMM) to detect partially methylated domains (PMDs) in Bis-seq data.

### Value

A GRangesList 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.

### Author(s)

Kamal Kishore

### See Also

`findDMR`

### Examples

    require(BSgenome.Hsapiens.UCSC.hg18)
    uncov_GR <- GRanges(Rle('chr20'), IRanges(c(14350,69251,84185), c(18349,73250,88184)))
    H1data <- system.file('extdata', 'H1_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe')
    H1.db <- BSdata(file=H1data, uncov=uncov_GR, org=Hsapiens)
    PMDs <- findPMDs(H1.db, Nproc=1, Chrs="chr20")

[Package methylPipe version 1.20.0 Index]