computeMethylationDataCoverage: Compute methylation data coverage
In DMRcaller: Differentially Methylated Regions caller

Description Usage Arguments Value Author(s) See Also Examples

This function computes the coverage for bisulfite sequencing data. It returns a vector with the proportion (or raw count) of cytosines that have the number of reads higher or equal than a vector of specified thresholds.

1 2	computeMethylationDataCoverage(methylationData, regions = NULL, context = "CG", breaks = NULL, proportion = TRUE)

`methylationData`	the methylation data stored as a `GRanges` object with four metadata columns (see `methylationDataList`).
`regions`	a `GRanges` object with the regions where to compute the coverage. If `NULL`, the coverage is computed genome-wide.
`context`	the context in which the DMRs are computed (`"CG"`, `"CHG"` or `"CHH"`).
`breaks`	a `numeric` vector specifing the different values for the thresholds when computing the coverage.
`proportion`	a `logical` value indicating whether to compute the proportion (`TRUE`) or raw counts (`FALSE`).

a vector with the proportion (or raw count) of cytosines that have the number of reads higher or equal than the threshold values specified in the breaks vector.

Nicolae Radu Zabet and Jonathan Michael Foonlan Tsang

plotMethylationDataCoverage, methylationDataList

# load the methylation data
data(methylationDataList)

# compute coverage in CG context
breaks <- c(1,5,10,15)
coverage_CG_wt <- computeMethylationDataCoverage(methylationDataList[["WT"]],
                 context="CG", breaks=breaks)

Loading required package: GenomicRanges
Loading required package: stats4
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Loading required package: IRanges
Loading required package: GenomeInfoDb