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)

[Package DMRcaller version 1.12.7 Index]