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NEW : SEQUENZA segmentation plainly implemented, for both L2R+BAF bivariate segmentation [Segment.SEQUENZA()] AND copy number estimation [ASCN.SEQUENZA()].
BUG : Segment.ff() : Corrected wrong do.call() call (parameters not given as a list).
CORR : ASCN.ASCAT() : CN output file was badly formatted.
MOD : ASCN.ff() : Suppressed the "segmenter" parameter, which is read from the RDS meta$eacon$segmenter value.
v0.3.2-1 (20180906) Bak2Skool
BUG : WES.Bin() : bin order was totally messed up when capture BED is not properly ordered (desynch due to bin name converted to factor, then levels replaced by mis-ordered rowname). This made WES.Normalize() stop at the GC/wave normalization step due to non-synched bin orders in data when compared to BINpack [Thx to Alexander Lefranc for reporting it] [fixed].
BUG : ASCN.ff() : fixed a bug in the do.call() call (arguments of ellipsis not converted to a list) [fixed].
CORR : ASCN.ff() : fixed the handling of out.dir sub() call.
CORR : README.md : Missing aroma.light dependency [Thx to Alexander Lefranc for reporting it, again].
ADD : ASCN.ff() : Added a control to check if provided segmentation RDS file is compatible with requested ASCN method.
MOD : Changed license to MIT.
v0.3.2 (20180808) PapeMamiePichine
ADD : FACETS segmentation plainly implemented, for both L2R+BAF bivariate segmentation AND copy number estimation. Coincidentaly, some modifications were performed :
. Segment.ASCAT() and ASCN.ASCAT() wrappers have been renamed to generic Segment() and ASCN(), with a new "segmenter" parameter, to support both of ASCAT and FACETS.
. Help functions for all segmentation / ASCN functions have been updated.
v0.3.1 (20180731) Recalcitrante
ADD : New feature : preparing the inclusion of FACETS segmentation methods.
. This required to include some additional data in the normalized RDS.
v0.3.0-1 (20180725) BzzzzSnap!
BUG : BINpack.maker() : subfunction failed to load the foreach package [fixed].
BUG : WES.Bin() : BAM indexation failed [fixed].
BUG : ASCN.ASCAT.ff() : Typo in dirname replacement made it non functional [fixed].
BUG : OS.Process() : chromosomes cutting with mingap failed due to calling an inexisting column [fixed].
ADD : Added a control on list type for functions that require a 'data' object as first parameter.
