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)

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