methylPipe (version 1.6.2)

profileDNAmetBin: Profile DNA methylation data for a set of genomic regions

Description

Profile the absolute and relative density of mC sites for each bin of each genomic region of a GEcollection object.

Usage

profileDNAmetBin(GenoRanges, Sample, mcCLASS="mCG",
mC=1, depthThr=0, mCpv=1, minCoverage=0.75, nbins = 2)
profileDNAmetBinParallel(GenoRanges, Sample, mcCLASS="mCG", mC=1,
depthThr=0, mCpv=1, minCoverage=0.75, Nproc=1, nbins = 2)

Arguments

GenoRanges

an object of class GRanges

Sample

an object of class BSdata

mcCLASS

character; one of: mCG, mCHG, mCHH

mC

numeric; the minumum number of reads with C (DNA-methylation events) at a given cytosine genomic position

depthThr

numeric; the minimum number of total reads at a given cytosine genomic position

mCpv

numeric; the minimum binomial pValue for an mC call at a given cytosine genomic position

minCoverage

numeric between 0 and 1; the minimum coverage of for the genomic region to be profiled; currently ignored

Nproc

numeric; the number of processor for parallelization

nbins

numeric; the number of bins each genomic region is divided

Value

• An object of class GRanges from which an object of class GEcollection is created with the binC, binmC and binrC data slots been filled with density matrices. These matrices report the density of mC sites in the sequence context specified by mcCLASS. They are counted for each bin in each genomic region and their count is divided by the bin size in bp. The binC data slot is filled with the density of all possible methylation sites in the specified sequence context. The binmC data slot is filled with the density of mC sites in the specified sequence context for the considered sample. The binrC data slot is filled with the ratio of binC and binmC matrices, representing the relative methylation for each bin in each genomic region.

Details

For each bin of each genomic region of a GRanges object, the absolute and relative density of mC sites is determined and an object of class GEcollection is created.

Examples

require(BSgenome.Hsapiens.UCSC.hg18)
H1data <- system.file('extdata', 'H1_chr20_CG_10k_tabix_out.txt.gz', package='methylPipe')
uncov_GR <- GRanges(Rle('chr20'), IRanges(c(14350,69251,84185), c(18349,73250,88184)))
H1.db <- BSdata(file=H1data, uncov= uncov_GR, org=Hsapiens)
gr_file <- system.file('extdata', 'GR_chr20.Rdata', package='methylPipe')
load(gr_file)
gec.H1 <- profileDNAmetBin(GenoRanges=GR_chr20, Sample=H1.db, mcCLASS='mCG', nbins=2)
head(binmC(gec.H1))