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 write_bedgraphs(m = meth, output_dir = ".") # Metilene write_bedgraphs(m = meth, output_dir = ".", rm_NA = FALSE, metilene = TRUE,multiBed = "metline_ip", phenoCol = "Day")
We also support bigWig format.
write_bigwigs(meth, output_dir = ".", samp_names = NULL)