profileDNAmetBin: Profile DNA methylation data for a set of genomic regions
In kamalfartiyal84/methylPipe: Base resolution DNA methylation data analysis

Description Usage Arguments Details Value Author(s) Examples

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

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)

`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

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.

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.

Mattia Pelizzola, Kamal Kishore

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))