Read Bismark

Share:

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

1

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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
# 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"]])