readBismark: Reads cytosine methylation stati determined by Bismark
In BiSeq: Processing and analyzing bisulfite sequencing data

Description Usage Arguments Details Value Author(s) References See Also Examples

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

1	readBismark(files, colData)

`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`.

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.

A BSraw object storing coverage and methylation information.

Hans-Ulrich Klein

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

BSraw-class

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