NEWS
methylSig 0.99.0 (2020-03-23)
- Refactor functions and workflow from pre-0.99.0 releases
o methylSigReadData() replaced with the functions:
o bsseq::read.bismark()
o filter_loci_by_coverage()
o filter_loci_by_location()
o methylSigTile() replaced with the functions:
o tile_by_regions()
o tile_by_windows()
o Differential testing should be preceded with:
o filter_loci_by_group_coverage()
o binomialDiffCalc() is replaced by diff_binomial()
o methylSigCalc() is replaced by diff_methylSig()
o methylSigDSS() is replaced by diff_dss_fit() and diff_dss_test()
- See "Using methylSig" vignette for full example.
- See "Updating methylSig Code" vignette for how to retrofit pre-0.99.0 code.