computeMethylationDataCoverage {DMRcaller}

R Documentation

Compute methylation data coverage

Description

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.

Usage

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

Arguments

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).

Value

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.

Author(s)

Nicolae Radu Zabet and Jonathan Michael Foonlan Tsang

See Also

plotMethylationDataCoverage, methylationDataList

Examples

# 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)

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