readBismark {BiSeq} | R Documentation

## 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`.

### 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.

### Value

A `BSraw` object storing coverage and methylation information.

### Author(s)

Hans-Ulrich Klein

### 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"))

[Package BiSeq version 1.27.3 Index]