Package: aroma.cn
=================

Version: 1.3.3 [2013-04-22]
o CLEANUP: findNeutralCopyNumberState() is now in PSCBS.
o Utilizing new startupMessage() of R.oo.


Version: 1.3.2 [2013-04-22]
o Updated package dependencies.
o CLEANUP: No longer using deprecated PSCBS methods.
o ROBUSTNESS: (load|save)Cache() from R.cache are now explicitly
  imported in the namespace.


Version: 1.3.1 [2013-01-17]
o Updated internal methods for PairedPSCBS to recognize when other
  mean-level estimators than the sample mean have been used.


Version: 1.3.0 [2013-01-07]
o Bumped up the package dependencies.
o BUG FIX: process() for PairedPscbsCaller used the global 'verbose'.


Version: 1.2.20 [2012-12-19]
o BUG FIX: Some example() scripts used non-defined values.


Version: 1.2.19 [2012-11-26]
o Bumped up the package dependencies.


Version: 1.2.18 [2012-11-21]
o Now applicable classes utilize the new ParametersInterface.
o DOCUMENTATION: Hiding more internal methods from the help indices.


Version: 1.2.17 [2012-11-13]
o CLEANUP/FIX: Used "cache:" field modified instead of "cached:".
  After correction, all clearCache() methods could be dropped.


Version: 1.2.16 [2012-11-12]
o CLEANUP: Now seq_along(x) instead of seq(along=x) everywhere.
  Similarly, seq(ds) where 'ds' is GenericDataFileSet is now
  replaced by seq_along(ds).  Likewise, seq_len(x) replaces 
  seq(length=x), and length(ds) replaces nbrOfFiles(ds).


Version: 1.2.15 [2012-11-05]
o CLEANUP: Replaced all whichVector() with which(), because the
  latter is now the fastest again. 


Version: 1.2.14 [2012-11-01]
o ROBUSTNESS: Now package also imports PSCBS to please 'R CMD check'.
  The reason was that some of the internal methods call PSCBS
  methods, which only happens if PSCBS is loaded in the first place
  but 'R CMD check' cannot known that.


Version: 1.2.13 [2012-10-29]
o CLEANUP: Now using Arguments$get(Read|Writ)ablePath() instead of
  filePath(..., expandLinks="any").


Version: 1.2.12 [2012-10-21]
o ROBUSTNESS: Now using Arguments$getWritablePath() everywhere instead
  of mkdirs(), because the former will do a better job in creating
  and asserting directories on slow shared file systems, and when it
  fails it gives a more informative error message.


Version: 1.2.11 [2012-10-17]
o ROBUSTNESS: Now all static Object methods that calls "next" methods,
  utilizes NextMethod(), which became possible with R.oo v1.10.0.


Version: 1.2.10 [2012-10-16]
o ROBUSTNESS/BUG FIX: No longer passing '...' to NextMethod(), cf.
  R-devel thread 'Do *not* pass '...' to NextMethod() - it'll do it 
  for you; missing documentation, a bug or just me?' on Oct 16, 2012.


Version: 1.2.9 [2012-10-11]
o Added getOutputFileClass() and getOutputFileExtension() for
  TotalCnSmoothing.


Version: 1.2.8 [2012-09-23]
o More internal updates.


Version: 1.2.7 [2012-09-20]
o Now PairedPscbsCaller() passes '...' to the internal callers,
  which makes it possible to for instance specify the number of
  bootstrap samples done for the AB caller.
o Now PairedPscbsModel() excludes the actual gaps from the known
  segments it passes to segmentByPairedPSCBS().


Version: 1.2.6 [2012-09-19]
o Added trial version of PairedPscbsCaller.
o Additional internal updates.
o BUG FIX: callPeaks(..., flavor="all") for PeaksAndValleys would
  return an error.


Version: 1.2.5 [2012-09-16]
o Added calculateTumorPSCNByGenotype().


Version: 1.2.4 [2012-09-15]
o Now fit() for PairedPscbsModel generates pair names iff tumor and
  normal names don't match, e.g. 'GSM517071_vs_GSM517072' (if match
  then just 'Patient1').  It also generated "pair" tags.
o Bumped up the package dependencies.


Version: 1.2.3 [2012-09-05]
o Bumped up the package dependencies.


Version: 1.2.2 [2012-08-26]
o Bumped up the package dependencies.
o DOCUMENTATION: Improved help on TotalCnBinnedSmoothing.


Version: 1.2.1 [2012-07-22]
o Added trial version of PairedPscbsModel.


Version: 1.2.0 [2012-06-05]
o Adopted findAtomicAberrations() for CBS from ditto of PairedPSCBS.
o GENERALIZATION: Now plotTracks() for PruneCNA supports CBS 
  segmentation results in additional to PairedPSCBS ones.
o GENERALIZATION: Now pruneCNA() is implemented for AbstractCBS,
  not just PairedPSCBS objects.
o Merged updates for findAtomicAberrations() for PairedPSCBS and
  some additional internal "equality" test functions.
o Updated package dependencies.


Version: 1.1.1 [2012-04-16]
o Updated package dependencies.


Version: 1.1.0 [2012-04-10]
o Updated package dependencies.


Version: 1.0.6 [2012-03-30]
o Added help for normalizePrincipalCurve().


Version: 1.0.5 [2012-03-06]
o BUG FIX: One of the PSCBS examples gave an error.


Version: 1.0.4 [2012-02-27]
o BUG FIX: drawC1C2Density() for PairedPSCBS would throw an exception
  if there was only one segment, or less than two finite (C1,C2):s.


Version: 1.0.3 [2012-02-24]
o CLEANUP: Moved some internal functions to the PSCBS package,
  so package dependencies was also updated.


Version: 1.0.2 [2012-02-23]
o Updated package dependencies.
o Additional internal updates.


Version: 1.0.1 [2012-01-16]
o Added TotalCnBinnedSmoothing().


Version: 1.0.0 [2012-01-11]
o ROBUSTNESS: Updated package dependencies.
o CLEANUP: The example code for the internal PairedPSCBS methods now
  only runs if environment variable _R_CHECK_FULL_ is set. This makes
  the package easier on the CRAN servers.


Version: 0.9.5 [2011-12-15]
o ROBUSTNESS: Now process() of TotalCnSmoothing writes atomically.
o Additional internal updates.


Version: 0.9.4 [2011-11-28]
o Updated package dependencies.
o Additional internal updates.


Version: 0.9.3 [2011-11-12]
o Updated the package dependencies.
o Some internal updates.


Version: 0.9.2 [2011-11-02]
o Updated the memoiziation keys for some of the PairedPSCBS
  methods so that results prior to PSCBS v0.13.3 will not
  be retrieved.


Version: 0.9.1 [2011-10-31]
o Added Rdoc comments to callPeaks() for PeaksAndValleys.


Version: 0.9.0 [2011-10-28]
o Added a namespace to the package, which will be more or less
  a requirement starting with R v2.14.0.


Version: 0.8.3 [2011-10-16]
o Now deShearC1C2(), translateC1C2() and transformC1C2() also 
  update C1 and C2 mean levels. 
o Now using getLocusData() and getSegments() internally for all
  PairedPSCBS objects whereever applicable.


Version: 0.8.2 [2011-08-07]
o The aroma.cn v0.8.1 tar ball uploaded to CRAN mistakenly
  contained a NAMESPACE file, which shouldn't have been there.


Version: 0.8.1 [2011-07-27]
o WORKAROUND: In order for the package to work with the most recent
  version of R devel, which automatically add namespaces to packages
  who do not have one, we explicitly have specify that this package
  should use cat() and getOption() of R.utils (instead of 'base').


Version: 0.8.0 [2011-07-10]
o CLEANUP: Removed some internal functions from the help index.
o FIXES: Forgot to update some examples and test scripts which
  were still referring to the old psCBS package (should be PSCBS).
o BUG FIX: Updated internal code to work with the new column names
  in PSCBS v0.11.0.


Version: 0.7.3 [2011-06-25]
o ROBUSTNESS: Updated package dependencies.
o FIXES: Now package refers to PSCBS package (not old psCBS).


Version: 0.7.2 [2011-04-03]
o CLEANUP: Utilizing hpaste() internally wherever applicable.


Version: 0.7.1 [2011-03-03]
o Fixed a small code typo that didn't make a difference.


Version: 0.7.0 [2011-01-19]
o Added beta classes PairedPSCBSFile and PairedPSCBSFileSet.
o Removed a NOTE from R CMD check.


Version: 0.6.4 [2010-11-04]
o ROBUSTNESS: Now all bootstrap methods utilize resample().
o Added more internal utility functions for future usage.


Version: 0.6.3 [2010-10-08]
o Added more internal utility functions for future usage.


Version: 0.6.2 [2010-09-24]
o Added more internal utility functions for future usage.


Version: 0.6.1 [2010-09-19]
o Added more internal utility functions for future usage.


Version: 0.6.0 [2010-09-15]
o Added internal utility functions for future usage.


Version: 0.5.2 [2010-08-04]
o Added option 'preserveScale' to TumorBoostNormalization for
  correcting for signal compression in heterozygous SNPs.
  The defaults is to do this correction.


Version: 0.5.1 [2010-07-25]
o callXXorXY() no longer calls gender from chr Y when gender is
  estimated as 'XX' from chr X.


Version: 0.5.0 [2010-05-14]
o Package submitted to CRAN.
o Updated citation information.
o Package now requires aroma.core v1.6.0.
o Package pass R CMD check on R v2.11.0 and v2.12.0 devel. 


Version: 0.4.7 [2010-04-04]
o Moved normalizeDifferencesToAverage(), normalizeTumorBoost(), 
  callNaiveGenotypes() and internal findPeaksAndValleys()
  to aroma.light v1.5.3.


Version: 0.4.6 [2010-03-18]
o BUG FIX: For flavors "v2" and "v3", normalizeTumorBoost() could
  introduce NaN:s if betaN was exactly zero or exactly one.


Version: 0.4.5 [2010-01-14]
o Added (for now internal) option to change the degrees of freedom
  of the fitted principal curves in MSCN.
o Added plotSmoothedPairsOne() to MultiSourceCopyNumberNormalization.


Version: 0.4.4 [2010-01-05]
o Added support for transform/untransform functions h(.) and g(.) to
  AbstractCurveNormalization, which allows us to fit say on the log
  scale, e.g. h(x)=log2(x), g(y)=2^y.
o BUG FIX: getOutputDataSet() of AbstractCurveNormalization returned 
  all files, not just the ones matching the input set.


Version: 0.4.3 [2010-01-01]
o ROBUSTNESS: Using new Arguments$getInstanceOf() were possible.
o ROBUSTNESS: Now all index arguments are validated correctly 
  using the new 'max' argument of Arguments$getIndices().  Before
  the case where "max == 0" was not handled correctly.  


Version: 0.4.2 [2009-12-09]
o Made flavor="v4" of TumorBoostNormalization the default, and if 
  used then no "flavor" tag is added.


Version: 0.4.1 [2009-11-03]
o Now callXXorXY() and callNaiveGenotypes() handles
  missing values and non-finite values.  They also
  censor outliers to become infinite/extreme values.
o Added callXXorXY().
o Added an example() to the Rd help of callNaiveGenotypes().
o Added Rd help to findPeaksAndValleys().
o Now argument 'tol' of findPeaksAndValleys() can be zero;
  before it had to be at least the smallest possible double.


Version: 0.4.0 [2009-11-01]
o CLEAN UP: Removed suggested dependency on princurve, which is
  now indirectly suggested/requested via aroma.light.
o More recent dependencies on Bioconductor packages.
o Package passes R CMD check on R v2.10.0.


Version: 0.3.8 [2009-10-10]
o Added normalizeTumorBoost() for RawAlleleBFractions.
o Added callGenotypes() for RawAlleleBFractions.
o Added RawGenotypeCalls. 


Version: 0.3.7 [2009-10-02]
o CLEAN UP: Updated to use byPath() instead fromFiles().


Version: 0.3.6 [2009-09-30]
o Renamed argument 'alignByChromosome' for the constructor of the
  MultiSourceCopyNumberNormalization class to "align" in order to
  allow for more types of aligned.
o UPDATE: The alignment of MultiSourceCopyNumberNormalization is now
  done using normalizeDifferencesToAverage(), which is robust against
  outliers and waviness etc.  The previous method which normalized
  toward the same overall median is no longer available.
o Added normalizeDifferencesToAverage().
o BUG FIX: getTags() of MultiSourceCopyNumberNormalization would return
  all asterisk tags as merged, e.g. c("mscn,align", "tagA", "tagB").


Version: 0.3.5 [2009-07-15]
o ADDED: XYCurveNormalization and PrincipalCurveNormalization.
o BUG FIX: TumorBoostNormalization: the 'srcFiles' attribute in file
  footer of the result files contained a duplicated default footer 
  instead of the tumor-normal pair.


Version: 0.3.4 [2009-07-08]
o ADDED: low-level callNaiveGenotype() and normalizeTumorBoost().


Version: 0.3.3 [2009-07-02]
o Added model 'flavor' "v4" which corrects heterozygots according 
  to "v2" and homozygotes according to "v1".
o Added new model flavor ("v3") of TumorBoostNormalization that is 
  an extension of last weeks model flavor.


Version: 0.3.2 [2009-06-23]
o Added an optional flavor ("v2") of TumorBoostNormalization that 
  avoids over correcting (especially at the heterozygotes), but 
  adjusting the correction factor.  Use argument flavor="v2".


Version: 0.3.1 [2009-06-08]
o UPDATE: The constructor of TumorBoostNormalization now only takes an
  AromaUnitGenotypeCallSet for argument 'gcN'.  It no longer takes an
  AromaUnitFracBCnBinarySet object, which was only an ad hoc solution.


Version: 0.3.0 [2009-05-29]
o ROBUSTNESS: Now all constructors report on unknown arguments.
o ROBUSTNESS: Now MultiSourceCopyNumberNormalization first write
  normalized data to a temporary file, which is then renamed. This
  lower the risk for having incomplete data in case of interrupts.
o Now getOutputDataSets() of  MultiSourceCopyNumberNormalization only
  returns output data files with a matching fullname in the input set.
o Added argument 'alignByChromosomes' to MultiSourceCopyNumberNormalization.
  If TRUE, the signals are shifted per chromosome such that the mean 
  of the normalized smoothed signals is the same for all sources.
  This can for instance remove systematic effects on sex chromosomes
  added by some ad hoc preprocessing methods.
o Added a clearCache() to MultiSourceCopyNumberNormalization.
o ALPHA: Added TumorBoostNormalization.
o INTERNAL: Added foundations for TumorBoost, i.e. in 
  memory classes such as TotalAndFracBSnpData.
o INTERNAL: Added findPeaksAndValleys().
o BUG FIX: Added missing argument 'verbose' in getTargetPositions() of
  TotalCnSmoothing.  This caused unwanted verbose output in some cases.
o BUG FIX: process() of TotalCnSmoothing would not "recognize" fullname
  translators, that is, the output filenames were always identical to 
  the input ones.
o Package pass R CMD check and all redundancy tests.


Version: 0.2.2 [2009-02-23]
o Minor update in order to work with new RawGenomicSignals.


Version: 0.2.1 [2009-02-12]
o Added redundancy tests to package.
o Further cleanup.  Some functions are now in aroma.light.


Version: 0.2.0 [2009-01-26]
o Adopted the package to the new classes of aroma.core.
o Several classes and methods were moved to aroma.core v1.0.0.
o {fit|backtransform}PrincipalCurve() were moved to aroma.light v1.11.1.


Version: 0.1.7 [2008-10-07]
o ALPHA: Added backtransformPrincipalCurve().


Version: 0.1.6 [2008-08-18]
o Added alpha version of MultiSourceCopyNumberNormalization.


Version: 0.1.5 [2008-07-30]
o Fixed some broken cross links in the Rd help.
  Package pass R CMD check on R v2.7.1 and v2.8.0.


Version: 0.1.4 [2008-06-12]
o Now extractRawCopyNumbers() of AromaTotalCnBinaryFile adds 
  annotation data fields to the returned object, e.g. platform, 
  chipType, and the fullname of the source file.


Version: 0.1.3 [2008-05-28]
o ALPHA: Added normalizePrincipalCurve() and fitPrincipalCurve().


Version: 0.1.2 [2008-05-22]
o ALPHA: Added extractRawCopyNumbers() to AromaTotalCnBinaryFile.
o ALPHA: Added TotalCnSmoothing.


Version: 0.1.1 [2008-05-18]
o Package now provides platform-independent classes 
  Aroma{Total|FreqB}CnSignal{File|Set}.   With the more generalized
  aroma.core package, it is now possible retrieve the AromaUgpFile
  for the above.  This provides the necessary basic methods for 
  plotting data along chromosomes.


Version: 0.1.0 [2008-05-09]
o Created.