readBismark: Reads cytosine methylation stati determined by Bismark

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

Description

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

Usage

1
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

1
2
3
file <- system.file("extdata", "CpG_context_test_sample.cov", package = "BiSeq")
rrbs <- readBismark(file,
                    colData= DataFrame(row.names="sample_1"))

BiSeq documentation built on May 6, 2019, 3:55 a.m.