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"]])

---