readBismark {DMRcaller} | R Documentation

## Read Bismark

### Description

This function takes as input a CX report file produced by Bismark and returns a `GRanges` object with four metadata columns The file represents the bisulfite sequencing methylation data.

### Usage

    readBismark(file)

### Arguments

`file` | The filename (including path) of the methylation (CX report generated by 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 one datasets into a file
    saveBismark(methylationDataList[["WT"]], "chr3test_a_thaliana_wt.CX_report")

    # load the data
    methylationDataWT <- readBismark("chr3test_a_thaliana_wt.CX_report")

    #check that the loading worked
    all(methylationDataWT == methylationDataList[["WT"]])

[Package DMRcaller version 1.18.0 Index]