06-Export.Rmdmethrix has multiple options to export data for different purposes. The write_bedgraph function supports a bedgraph format, that can be directly uploaded to UCSC. The multibed option generates a file with all samples as columns. The metilene option ensures that this file is in the correct format for metilene, a command line DMR caller.
# UCSC browser style write_bedgraphs(m = meth, output_dir = "./")
We also support bigWig format.
write_bigwigs(meth, output_dir = "./", samp_names = NULL)