Pull Bioc_3_10 into master for Bioconductor submission - Githubissues

sartorlab / methylSig

R package for DNA methylation analysis

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Pull Bioc_3_10 into master for Bioconductor submission #41

Closed rcavalcante closed 4 years ago

rcavalcante commented 4 years ago

Changes in 0.99.0 (2020-03-23)

Refactor functions and workflow from pre-0.99.0 releases
- methylSigReadData() replaced with the functions:
- bsseq::read.bismark()
- filter_loci_by_coverage()
- filter_loci_by_location()
- methylSigTile() replaced with the functions:
- tile_by_regions()
- tile_by_windows()
- Differential testing should be preceded with:
- filter_loci_by_group_coverage()
- binomialDiffCalc() is replaced by diff_binomial()
- methylSigCalc() is replaced by diff_methylSig()
- 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.