Package: QDNAseq
================

Version: 0.99.4 [2014-03-25]
o Make R.cache an optional instead of required package, as it is only needed
  when binReadCounts() is run with with caching turned on.


Version: 0.99.3 [2014-03-13]
o Fix imports.
o Change coding style of intendation for one leftover file.


Version: 0.99.2 [2014-03-12]
o Added biocViews.
o Added more examples to manual pages.
o Updated NAMESPACE imports.
o Changed coding style of intendation from two to four spaces.


Version: 0.99.1 [2014-03-11]
o Added runnable examples to manual pages.


Version: 0.99.0 [2014-03-11]
o Added parameter scale to plot() to specify whether output should be scale
  according to chromosome sizes (default is TRUE).
o Version number bumped to 0.99.0 for Bioconductor.


Version: 0.8.0 [2014-03-07]
o Added more information to the manual pages.


Version: 0.7.7 [2014-02-24]
o Added the value of expected standard deviation (based on sequence depth)
  to copy number profile plots, and an option to choose which labels to to show
  along the x-axis of noisePlot(): average number of reads per bin, its
  reciprocal, or total number of reads.


Version: 0.7.6 [2014-02-20]
o Added a new function for calculating standard deviations using a trimmed
  (default 0.1%) first-order estimator.


Version: 0.7.5 [2014-02-06]
o Introduced smoothOutlierBins() and normalizeSegmentedBins() as separate
  functions instead of them being parts of normalizeBins() and segmentBins().
o Renamed readCountPlot() to isobarPlot() and added an option to plot loess
  fits and residuals in addition to median read counts.
o Standard deviation in the top-right corner of profile plots is now calculated
  without taking a log2-tranformation.
o DOCUMENTATION: Updates to the manual pages and vignette.


Version: 0.7.0 [2014-01-28]
o QDNAseqCopyNumbers now stores all signals on the original non-log scale.
o Now using classes QDNAseqReadCounts and QDNAseqCopyNumbers which both
  inherits from QDNAseqSignals.


Version: 0.6.3 [2014-01-25]
o Added support for coercing an QDNAseqReadCounts object to an
  CGHcall::cghRaw object via as(x, "cghRaw") and similar for coercing
  to cghSeg and cghCall.
o Added argument 'filter' to makeCgh() to control whether to drop
  "filtered" bins from the created object or not.
o ROBUSTNESS: Now makeCgh() gives a more informative error message when
  it fails to create a CGHcall::cgh* object.
o DOCUMENTATION: Added more information to the help for QDNAseqReadCounts,
  binReadCounts(), correctBins() and normalizeBins().


Version: 0.6.2 [2014-01-21]
o Added argument 'offset=2^-10' to compareToReference().  Previously,
  the default behavior corresponded to offset=1.
o DOCUMENTATION: Added more on help for makeCgh().


Version: 0.6.1 [2014-01-13]
o Now normalizeBins(..., logTransform=FALSE) scales the signals toward
  the target (mean, median or mode) rather than shifts them, which is the
  case when logTransform=TRUE.
o Added support for method="mean" of normalizeBins().
o Now normalizeBins() passes '...' to DNAcopy::smooth.CNA().
o DOCUMENTATION: Added help details on arguments of binReadCounts()
  and normalizeBins().


Version: 0.6.0 [2013-11-22]
o Improved correction for GC content and mappability.
o Revamped caching of intermediate files.


Version: 0.5.8 [2013-11-16]
o Now it is possible to disable verbose message, i.e.
  options('QDNAseq::verbose'=FALSE).


Version: 0.5.7 [2013-11-04]
o ...


Version: 0.5.6 [2013-10-31]
o Added a NEWS file (this file).
o Cleaned up and updated package dependencies.


Version: 0.5.0 [2013-10-18]
o ...


Version: 0.4.2 [2013-08-30]
o ...


Version: 0.4.0 [2013-08-19]
o ...


Version: 0.3.2 [2013-08-05]
o ...


Version: 0.2.0 [2013-06-23]
o ...


Version: 0.1.0 [2013-05-06]
o Added package to repository.


