Identifying Partially Methylated Domains (PMDs)
This function is a wrapper function to identify partially methylated domains (PMDs) in Bis-seq data.
An object of class BSdataSet
numeric; the number of processors to use, one chromosome is ran for each processor
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.
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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")
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