findPMDs: Identifying Partially Methylated Domains (PMDs)
In kamalfartiyal84/methylPipe: Base resolution DNA methylation data analysis

Description Usage Arguments Details Value Author(s) See Also Examples

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

1 2	## S4 method for signature 'methylPipe,BSdata' findPMDs(Object, Nproc=1, Chrs=NULL)

`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

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.

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.

Kamal Kishore

findDMR

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")