Started a migration of the CoMeth class to a VIRTUAL class. Implementing concrete instances (and associated methods) for particular size m-tuples, e.g. CoMethI for 1-tuples.
Implemented CoMeth VIRTUAL class and concrete subclasses CoMeth1, CoMeth2 and CoMeth3Plus.
All tests pass and R CMD CHECK succeeds (with warnings).
Fix error in test of getPos
Defined the MethylationLociSet class and began defining some of the associated methods.
Began re-formatting .R to have consistent style.
Added code to create makeMLS function.
Added (unexported) fread.comethylation, which is "data.table::fread"-based. This is faster than read.comethylation but has a few limitations, which is why it is not yet exported.
Fix to .travis.yml to depend required Bioconductor packages.
Fix to .travis.yml so that required Bioconductor packages are installed.
Fix merge conflict
another fix to .travis.yml to get Bioconductor packages installed
Fixed major bug in how LOR is computed. Added test of of the original bug but more unit tests required.
Made sure fread.comethylation doesn’t delete the original file if passed a gzip.
Changes to work the development version of Bioconductor rather than the current release.
Changes to "comparison" methods to avoid the bug I reported in https://stat.ethz.ch/pipermail/bioc-devel/2014-May/005820.html (thanks to Hervé Pagès for making the required changes to GenomicRanges).
Fixed .travis.yml
Switched Imports from BSgenome to GenomeInfoDb.
Now Suggests BSgenome.Celegans.UCSC.ce10 and BSgenome.Hsapiens.UCSC.hg19, as I'll probably use these in vignettes.
Began function to compute correlations of beta-values.
Wrote the first of two internal functions used to compute the actual correlations.
Separated the making of "valid pairs" from the computation of beta-value correlations.
Sketched remainder of betaCor() functionality.
Removed redundant sort in .autoCorVP().
Return the fsipdc levels from both .autoCorVP() and .generalNILVP().
Added within-sample correlation computations for "valid pairs" in betaCor().
Added a show method for BetaCor.
Added read.mbias function.
Make "CpG" -> "CG" for consistency.
Fix missing Suggests