getCoverage: Obtain coverage for BSseq objects.
In bsseq: Analyze, manage and store bisulfite sequencing data

Description Usage Arguments Value Author(s) See Also Examples

Obtain coverage for BSseq objects.

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getCoverage(BSseq, regions = NULL, type = c("Cov", "M"),
  what = c("perBase", "perRegionAverage", "perRegionTotal"),
  withDimnames = TRUE)

`BSseq`	An object of class `BSseq`.
`regions`	An optional `data.frame` or `GenomicRanges` object specifying a number of genomic regions.
`type`	This returns either coverage or the total evidence for methylation at the loci.
`what`	The type of return object, see details.
`withDimnames`	A `logical(1)`, indicating whether dimnames should be applied to extracted coverage elements. Setting `withDimnames = FALSE` increases the speed and memory efficiency with which coverage is extracted.

NOTE: The return type of getCoverage varies depending on its arguments.

If regions are not specified (regions = NULL) a DelayedMatrix object (what = "perBase") is returned. This will either contain the per-base coverage, the average coverage, or the genome total coverage (depending on value of what).

If what = "perBase" and regions are specified, a list is returned. Each element of the list is a DelayedMatrix object corresponding to the genomic loci inside the region. It is conceptually the same as splitting the coverage by region.

If what = "perRegionAverage" or what = "perRegionTotal" and regions are specified the return value is a DelayedMatrix object. Each row of the DelayedMatrix corresponds to a region and contains either the average coverage or the total coverage in the region.

Kasper Daniel Hansen khansen@jhsph.edu.

BSseq for the BSseq class.

data(BS.chr22)
head(getCoverage(BS.chr22, type = "M"))
reg <- GRanges(seqnames = c("chr22", "chr22"),
  ranges = IRanges(start = c(1, 2*10^7), end = c(2*10^7 +1, 4*10^7)))
getCoverage(BS.chr22, regions = reg, what = "perRegionAverage")
  cList <- getCoverage(BS.chr22, regions = reg)
length(cList)
head(cList[[1]])

#-------------------------------------------------------------------------------
# An example using a HDF5Array-backed BSseq object
#

library(HDF5Array)
# See ?SummarizedExperiment::saveHDF5SummarizedExperiment for details
hdf5_BS.chr22 <- saveHDF5SummarizedExperiment(x = BS.chr22,
                                              dir = tempfile())
head(getCoverage(hdf5_BS.chr22, type = "M"))
reg <- GRanges(seqnames = c("chr22", "chr22"),
               ranges = IRanges(start = c(1, 2 * 10 ^ 7),
               end = c(2 * 10 ^ 7 + 1, 4 * 10 ^ 7)))
getCoverage(hdf5_BS.chr22, regions = reg, what = "perRegionAverage")
hdf5_cList <- getCoverage(hdf5_BS.chr22, regions = reg)
length(hdf5_cList)
head(hdf5_cList[[1]])