Bismark is a bisulfite read mapper and methylation caller. This method reads Bismark's
output files and returns a
Samples' names plus additional sample information
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
This will output two files, a
.bedGraph and a
We will import the
colData argument should specify the sample names as
character. Alternatively, a
DataFrame can be given. Then, the row names are used as
sample names and the data frame is passed to the final
BSraw object storing coverage and methylation information.
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