readBismarkPool {DMRcaller} | R Documentation

## Read Bismark pool

### Description

This function takes as input a vector of CX report file produced by Bismark and returns a `GRanges` object with four metadata columns (see `methylationDataList`). The file represents the pooled bisulfite sequencing data.

### Usage

    readBismarkPool(files)

### Arguments

`files` | The filenames (including path) of the methylation (CX report generated with Bismark) to be read

### Value

the methylation data stored as a `GRanges` object with four metadata columns (see `methylationDataList`).

### Author(s)

Nicolae Radu Zabet and Jonathan Michael Foonlan Tsang

### Examples

    # load methylation data object
    data(methylationDataList)

    # save the two datasets
    saveBismark(methylationDataList[["WT"]],
               "chr3test_a_thaliana_wt.CX_report")
    saveBismark(methylationDataList[["met1-3"]],
               "chr3test_a_thaliana_met13.CX_report")

    # reload the two datasets and pool them
    filenames <- c("chr3test_a_thaliana_wt.CX_report",
                   "chr3test_a_thaliana_met13.CX_report")
    methylationDataPool <- readBismarkPool(filenames)

[Package DMRcaller version 1.24.0 Index]