version 1.5.0 - complete mouse array support and sesame/minfi compatability confirmed

v1.5.0

• MAJOR refactor/overhaul of all the internal classes. This was necessary to fully support the mouse array.
  • new SigSet class object that mirror's sesame's SigSet and SigDF object.
    • Combines idats, manifest, and sample sheet into one object that is inherited by SampleDataContainer
  • RawDataset, MethylationDataset, ProbeSubtype all deprecated and replaced by SigSet
  • SampleDataContainer class is now basically the SigSet plus all pipeline processing settings
  • new mouse manifest covers all probes and matches sesame's output
  • Processing will work even if a batch of IDATs have differing probe counts for same array_type, though those
    differing probes in question may not be saved.
  • unit tests confirm that methylprep, sesame, and minfi beta values output match to within 1% of each other now. Note that the intermediate stages of processing (after NOOB and after DYE) do not match
    with sesame in this version. Can be +/- 100 intensity units, likely due to differences in order of
    steps and/or oob/mask probes used.