Read Bismark pool

Share:

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

1

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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
# 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)