methylPipe (version 1.6.2)

findPMDs: Identifying Partially Methylated Domains (PMDs)

Description

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

Usage

## S3 method for class '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

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.

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.

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")