BiSeq (version 1.12.0)

readBismark: Reads cytosine methylation stati determined by Bismark

Description

Bismark is a bisulfite read mapper and methylation caller. This method reads Bismark's output files and returns a BSraw object.

Usage

readBismark(files, colData)

Arguments

files

A character pointing to cov files created by Bismark's methylation_extractor and bismark2bedGraph; see Details. This can be a compressed file (see file).

colData

Samples' names plus additional sample information as character, data.frame or DataFrame.

Value

BSraw object storing coverage and methylation information.

Details

Input files are created with Bismark as follows (from the command line):

bismark_methylation_extractor -s --comprehensive test_sample.sam

bismark2bedGraph -o CpG_context_test_sample.bedGraph CpG_context_test_sample.txt

This will output two files, a .bedGraph and a .cov file. We will import the CpG_context_test_sample.cov using readBismark.

The colData argument should specify the sample names as character. Alternatively, a data.frame or DataFrame can be given. Then, the row names are used as sample names and the data frame is passed to the final BSraw object.

References

http://www.bioinformatics.bbsrc.ac.uk/projects/bismark/

See Also

BSraw-class

Examples

file <- system.file("extdata", "CpG_context_test_sample.cov", package = "BiSeq")
rrbs <- readBismark(file,
                    colData= DataFrame(row.names="sample_1"))