Package: PSCBS
==============

Version: 0.23.0 [2012-03-20]
o Added a package vignette.


Version: 0.22.2 [2012-02-29]
o BUG FIX: plotTracks(..., add=TRUE) for PairedPSCBS would add TCNs
  when BAFs and DHs where intended.


Version: 0.22.1 [2012-02-28]
o Updated package dependencies to R.rsp (>= 0.7.3) so that
  report() for PairedPSCBS no longer require non-public packages.
o Now it is possible to turn off usage of the alpha channel in
  plots generated by report(), which can be handy on systems where
  the default PNG device does not support the alpha channel.
  Example: setOption("PSCBS::report/useAlphaChannel", FALSE).


Version: 0.22.0 [2012-02-27]
o Added report() for PairedPSCBS.


Version: 0.21.0 [2012-02-27]
o Added argument 'fields' to getLocusData() for PairedPSCBS.
o Added renameChromosomes() to AbstractCBS.


Version: 0.20.0 [2012-02-26]
o Added alpha version of callGainNeutralLoss() for PairedPSCBS,
  which certainly will be updated in the future.  This caller
  is tested by the system tests.
o Added dropChangePoints() for AbstractCBS.
o Added some internal utility functions for PairedPSCBS taken
  from the aroma.cn package.  Some of these may become public
  later, but for they should be considered internal.
o ROBUSTNESS: Added more sanity checks validating the correctness 
  of what is returned by extractSegments() for CBS and PairedPSCBS.
o BUG FIX: extractSegments() for PairedPSCBS would return incorrect
  row indices, more precisely, overlapping data chunks.
o BUG FIX: bootstrapTCNandDHByRegion() for PairedPSCBS would resample
  from a subset of the intended TCNs, iff the DH mean was non-finite
  while there were still heterozygous SNPs.  This introduced a bias in
  the estimates, which was neglectable for large segments, but for very
  small segments (a few loci) it could be relatively large.


Version: 0.19.8 [2012-02-23]
o ROBUSTNESS: Package now explicitly depends on 'utils'.


Version: 0.19.7 [2012-02-22]
o BUG FIX: findLargeGaps() did not handle missing values for
  argument 'chromosome'.
o BUG FIX: segmentByCBS(..., knownSegments=knownSegments) would
  incorrectly throw a sanity-check exception if 'knownSegments'
  contains a segment with 'start' and 'stop' positions being equal.
o BUG FIX: Argument 'calls' of plotTracks() for PairedPSCBS was ignored
  if more than one chromosome was plotted.


Version: 0.19.6 [2012-01-24]
o ROBUSTNESS: Now getCallStatistics() for CBS asserts that calls have
  been made.  If not, an exception is thrown.


Version: 0.19.5 [2012-01-21]
o DOCUMENTATION: Added details to the help of callLOH() and callAB() on
  the difference between (AB,LOH)=(TRUE,FALSE) and (AB,LOH)=(TRUE,NA).
o Corrected some of verbose messages of estimateDeltaLOHByMinC1ForNonAB()
  for PairedPSCBS objects.


Version: 0.19.4 [2012-01-10]
o Now example(segmentByPairedPSCBS) and the system tests that are run
  by R CMD check are tuned to (by default) run much faster by segmenting
  using fewer data points and bootstrapping using fewer samples.  This
  update was done to meet the new CRAN policy.  By setting environment
  variable _R_CHECK_FULL_ to '1' the full data set is used instead.


Version: 0.19.3 [2012-01-09]
o ROBUSTNESS: Now extractSegments() for PairedPSCBS gives an informative
  error message that it is not supported if CNs were segmented using 
  flavor "tcn,dh".
o BUG FIX: postsegmentTCN() for PairedPSCBS could generate an invalid
  'tcnSegRows' matrix, where the indices for two consecutive segments
  would overlap, which is invalid.  Thanks to Minya Pu for reporting
  on failed sanity check related to this.


Version: 0.19.2 [2011-12-29]
o ROBUSTNESS: Explicitly added 'digest' to the list of suggested packages.


Version: 0.19.1 [2011-12-13]
o Added support for callGainsAndLosses(..., method="ucsf-dmad")
  of CBS objects.


Version: 0.19.0 [2011-12-12]
o Added optional argument 'indices' to getLocusData() to be able
  to retrieve the locus-level data as indexed by input data.
o BUG FIX: Now gapsToSegments() gave invalid segments for chromosomes
  with more than one gap.  Now gapsToSegments() validates argument 
  'gaps' and asserts that it returns non-overlapping segments.
o DOCUMENTATION: Clarified in help("segmentByCBS") how missing
  values are dealt with.


Version: 0.18.2 [2011-12-07]
o Now plotTracks() for CBS always returns an invisible object.
o BUG FIX: pruneBySdUndo() for CBS did not work with more than
  one array.


Version: 0.18.1 [2011-12-03]
o Added drawChangePoints() for AbstractCBS.
o Now pruneByHClust() for AbstractCBS updates the segment means.
o Added writeSegments() for PSCBS object.
o Now print() for AbstractCBS returns getSegments(..., simplify=TRUE).
o Added argument 'simplify' to getSegments().
o Added arguments 'name', 'tags' and 'exts' to writeSegments() and
  writeLocusData() and dropped 'filename'.


Version: 0.18.0 [2011-11-28]
o Added pruneByHClust() for AbstractCBS, with implementation
  for CBS and PairedPSCBS.
o extractCNs() for CBS would not return a matrix but a data.frame.
o BUG FIX: extractTotalCNs() for CBS would give an error.


Version: 0.17.4 [2011-11-26]
o Added argument 'updateMeans=TRUE' to callROH() for PairedPSCBS.
o Now bootstrapTCNandDHByRegion() for PairedPSCBS preserves NAs 
  for DH and (C1,C2) quantiles, if the DH mean level is NA, which
  can happen when a segment is called ROH.  This also makes sure
  that a segment called ROH will not be called AB.
o An internal sanity check of bootstrapTCNandDHByRegion() for
  PairedPSCBS would give an error if DH mean levels had been set
  to NA for segments called ROH.


Version: 0.17.3 [2011-11-24]
o Added callSegmentationOutliers() and dropSegmentationOutliers()
  for data frames.
o CLEANUP: Renamed field 'position' of the example data to 'x'.
  This helps us clean up some of the examples.
o BUG FIX: bootstrapTCNandDHByRegion() for PairedPSCBS would give
  an error, if a segment did not have any TCN signals, which can
  occur when known segments are specified for Paired PSCBS.


Version: 0.17.2 [2011-11-22]
o Added findLargeGaps() and gapsToSegments().


Version: 0.17.1 [2011-11-21]
o BUG FIX: The internal sanity check of testROH() on weights was
  slightly too conservative (required to high precision) when it
  came to asserting that the sum of the weights equals one.
o BUG FIX: resegment() for PairedPSCBS called segmentByCBS()
  instead of segmentByPairedPSCBS().


Version: 0.17.0 [2011-11-19]
o GENERALIZATION: Now it is possible to run Paired PSCBS (without
  TumorBoost) when only genotypes but not BAFs are available for the
  matched normal.


Version: 0.16.3 [2011-11-17]
o Added resegment() for CBS and PairedPSCBS for easy resegmentation.
o Adjusted segmentByCBS() such that it can handle 'knownSegments'
  with chromosome boundaries given as -Inf and +Inf.
o Now argument 'mar' for plotTracks() defaults to NULL.
o ROBUSTNESS: Added redundancy tests for segmentByCBS() and
  segmentByPairedPSCBS() with argument 'knownSegments'.
o ROBUSTNESS: Now segmentByCBS() does more validation of 'knownSegments'.
o FIX: extractRegions() for AbstractCBS would also show verbose output.
o BUG FIX: Now argument/parameter 'seed' is correctly preserved by
  segmentByCBS().  So is 'tbn' for segmentByPairedPSCBS().
o BUG FIX: segmentByPairedPSCBS() would give an error when trying to
  segment DH if the TCN segment contains no data points, which could
  happen if 'knownSegments' specifies an empty segment, e.g. centromere.
o BUG FIX: extractSegments() for CBS would throw an error when
  there were multiple chromosomes.


Version: 0.16.2 [2011-11-16]
o Now segmentByCBS(..., w) stores weights 'w', if given, in the 
  locus-level data table of the returned CBS object.
o Added pruneBySdUndo() for CBS, which does what undo.splits="sdundo"'
  for DNA::segment(), but on the already segmented results.
o Now updateMeans() uses locus-specific weights, iff available.
o Added updateBoundaries() for CBS to update (start,stop) per segment.
o CORRECTNESS: Now updateMeans() for CBS identifies loci via internal
  'segRows' field and no longer by locations of segment boundaries,
  which gave slightly incorrect estimates for "tied" loci.


Version: 0.16.1 [2011-11-15]
o Now more segmentation parameters are stored in the CBS object.
o SPEEDUP: Now segmentByCBS() will use memoization to retrieve 
  so called "sequential boundaries for early stopping", iff any of
  the DNAcopy::segment() arguments 'alpha', 'nperm' and 'eta' are
  specified.  See also DNAcopy::getbdry().
o Added method="DNAcopy" to estimateStandardDeviation() for CBS, which
  estimates the std. dev. using DNAcopy:::trimmed.variance().
o BUG FIX: extractSegments() for CBS would throw an error, because in
  most cases it would created a corrupt internal 'segRows' field.


Version: 0.16.0 [2011-11-12]
o Added argument 'oma' and 'mar' to plotTracksManyChromosomes() for
  PairedPSCBS for setting graphical parameters when 'add' == FALSE.
o Added callROH().
o Added arguments 'from' and 'adjustFor' to updateMeans().


Version: 0.15.5 [2011-11-04]
o BUG FIX: extractSegment() for AbstractCBS would give an error,
  because it called itself instead of extractSegments().


Version: 0.15.4 [2011-10-30]
o Added save() and load() methods to AbstractCBS, which are wrappers
  for saveObject() and loadObject() that assert the correct class
  structure.  Also, the load() method will automatically update the
  class hierarchy for CBS and PairedPSCBS objects that were saved
  before adding class AbstractCBS.


Version: 0.15.3 [2011-10-23]
o BUG FIX: callAmplifications() for CBS generated an error, if
  more than one chromosome were called.
o BUG FIX: The length of a segment must be defined as 'end-start' 
  and not 'end-start+1' so that the the total length of all segments
  adds up correctly.
o BUG FIX: highlightArmCalls() for CBS did not handle empty chromosomes.
o BUG FIX: getCallStatisticsByArms() for CBS would thrown a error if
  argument 'genomeData' did not contain exactly the same chromosomes
  as in the CBS object.


Version: 0.15.2 [2011-10-21]
o Added mergeThreeSegments() to AbstractCBS.
o BUG FIX: Recent updates caused segmentByPairedPSCBS(data) not to
  work when 'data' is a data frame.


Version: 0.15.1 [2011-10-21]
o By setting 'start' and 'end' to NAs in 'knownSegments' (chromosome must
  still be specified), it is possible to insert an empty segment that
  disconnects the two flanking segments, e.g. centromere and the two arms.


Version: 0.15.0 [2011-10-20]
o Added support for specifying priorly known segments, such as chromosome
  arms and centromeres, in segmentByCBS() via argument 'knownSegments'.
o CLEANUP: Dropped a stray debug output message in segmentByPairedPSCBS().


Version: 0.14.3 [2011-10-17]
o Added argument 'asMissing' to dropRegions() for AbstractCBS.


Version: 0.14.2 [2011-10-16]
o Implemented extractCNs() for CBS and PairedPSCBS.
o Added extractTotalCNs() for CBS.


Version: 0.14.1 [2011-10-14]
o Added implementation of extractRegions() for AbstractCBS, which
  utilizes extractSegments().
o Added abstract extractSegments() and extractSegment() for AbstractCBS.
o Now extractTCNAndDHs() for PairedPSCBS passes '...' to getSegments().


Version: 0.14.0 [2011-10-10]
o CLEANUP: Harmonization of several method names.
o CLEANUP: Internal restructuring of the source code files.


Version: 0.13.5 [2011-10-10]
o Added dropChangePoint() for AbstractCBS, which is just a
  "name wrapper" for mergeTwoSegments().
o Added dropRegion() and dropRegions() for AbstractPSCBS, where
  the former is a wrapper for the latter dropRegions().
o Added updateMeans() and mergeTwoSegments() for CBS in addition
  already available PairedCBS versions.
o Relabelled column 'id' to 'sampleName' returned by getSegments().
o ROBUSTNESS: Now using getSegments() everywhere possible.
o BUG FIX: For so called "splitter" rows, not all columns returned
  by getSegments() of CBS were missing values.
o BUG FIX: The object returned by as.CBS() of DNAcopy did not have the
  correct class hierarchy.


Version: 0.13.4 [2011-10-08]
o Added all.equal() for AbstractCBS, which does not compare attributes.
o Now internal getChromosomeRanges() of CBS returns a data.frame
  instead of a matrix, and first column is now 'chromosome'.
o Added optional argument 'regions' to getCallStatistics() of CBS
  in order to calculate call statistics on subsets of chromosomes,
  e.g. chromosome arms.
o Added drawChromosomes() for CBS.
o Added getCallStatisticsByArms(), callArms() and highlightArmCalls() 
  for CBS objects.


Version: 0.13.3 [2011-10-03]
o GENERALIZATION: Now segmentByCBS() and segmentByPairedPSCBS()
  also accepts a data.frame of locus-level data with column names
  matching the locus-level arguments accepted by the corresponding
  method.
o GENERALIZATION: Now all segmentation result classes (CBS and PSCBS)
  inherits from the AbstractCBS class, which provides methods such
  as getSampleName(), getChromosomes() and getSegments().
o DOCUMENTATION: Added lots of more help pages.
o CLEANUP: Dropped empty callSegments() for PairedPSCBS.


Version: 0.13.2 [2011-09-30]
o GENERALIZATION: Now drawLevels() for PairedPSCBS allows for drawing
  segmentation results in 'betaT' space.
o BUG FIX: plotTracks2(..., panels="dh") gave an error due to a
  forgotten assigment.


Version: 0.13.1 [2011-09-06]
o Added formal class CBS, which holds the segmentation results
  returned by segmentByCBS().  Several methods are available for
  CBS objects, e.g. nbrOfLoci(), nbrOfSegments(), nbrOfChromosomes(),
  getChromosomes(), estimateStandardDeviation() etc.
o Now segmentByCBS() always returns a CBS object.  To coerce to a
  DNAcopy object (as defined in the DNAcopy class) use as.DNAcopy().
o Added coerce methods as.DNAcopy() for CBS objects and as.CBS()
  for DNAcopy objects.


Version: 0.13.0 [2011-09-01]
o GENERALIZATION: Now segmentByCBS() can process multiple chromosomes.
o BUG FIX: Internal methods plotTracksManyChromosomes() and
  tileChromosomes() for CBS did not work at all and therefore
  neither plotTracks() for CBS with more than one chromosome.
o Added append() for CBS objects.


Version: 0.12.2 [2011-08-27]
o CLEANUP: Now R CMD check is no longer giving a note that the
  package loads package 'DNAcopy' in .onAttach().


Version: 0.12.1 [2011-08-08]
o BUG FIX: If dropSegmentationOutliers() would drop an outlier next to
  a change point, such that the total copy-number signal becomes NA,
  then the sanity checks that TCN segments always overlaps DH segments
  would fail.  Now the sanity checks are aware of this special case.
  These sanity checks were moved from bootstrapTCNandDHByRegion() to
  segmentByPairedPSCBS().  Thanks Christine To at University of Toronto
  for reporting on this.


Version: 0.12.0 [2011-07-23]
o Added a namespace to the package, which will be more or less
  a requirement in the next major release of R.
o BUG FIX: Recently R devel automatically adds a namespace to
  a package, if missing.  This caused some of the PSCBS examples
  to throw an exception related to incorrect dispatching of cat().


Version: 0.11.7 [2011-07-15]
o DOCUMENTATION: Added a section to help("segmentByPairedPSCBS") on
  the importance of doing a whole-genome PSCBS segmentations if 
  calling AB and LOH states afterward.
o DOCUMENTATION: Made it more clear in help("segmentByPairedPSCBS")
  that arguments 'betaT', 'betaN' and 'muN' may contain NAs for 
  non-polymorphic loci.


Version: 0.11.6 [2011-07-14]
o BUG FIX/ROBUSTNESS: In some cases, the segmentation table would 
  contain column names with incorrect capitalization, e.g. "tcnnbrOfLoci"
  instead of "tcnNbrOfLoci".  This would cause several downstream 
  methods to give an error.  The reason for this is that the Hmisc
  package, if loaded after R.utils, overrides capitalize() in R.utils
  with another (buggy?) capitalize() function.  To avoid this, we
  now everywhere specify explicitly that we want the one in R.utils.
  Thanks Christine To at University of Toronto for reporting on this.


Version: 0.11.5 [2011-07-10]
o ROBUSTNESS: Fixed partial argument matchings in arrowsC1C2() and
  arrowsDeltaC1C2() for PairedPSCBS.
o BUG FIX: tileChromosomes() for PairedPSCBS was still assuming the
  old naming convention of column names.  This caused plotTracks()
  to throw an exception when plotting multiple chromosomes.


Version: 0.11.4 [2011-07-07]
o GENERALIZATION: Now the internal estimator function that
  estimateDeltaLOH() uses returns -Inf if all segments are called AB,
  instead of throwing an exception.  This will in turn make callLOH()
  call all segments to be non-LOH.
o DOCUMENTATION: Removed obsolete references to the R-forge repository.
o BUG FIX: Consecutive calls to callAB(..., force=TRUE) would append
  additional 'abCall' columns to the segmentation table instead of
  replacing existing calls.


Version: 0.11.3 [2011-07-06]
o ROBUSTNESS: Added a sanity check to estimateDeltaLOHByMinC1AtNonAB() for
  PairedPSCBS object. The test asserts that there exist segments that are
  not in allelic balance, which are needed in order to estimate DeltaLOH.
o DOCUMENTATION: The description of argument 'chromosome' for 
  segmentByPairedPSCBS() did not describe how to segment multiple
  chromosomes in one call.


Version: 0.11.2 [2011-07-05]
o BUG FIX: Output fields 'tcnNbrOfSNPs'and 'tcnNbrOfHets' were 
  mistakenly labelled as 'tcnNbrOr...'.  Thanks Christine Ho at
  UC Berkeley for reporting on this.


Version: 0.11.1 [2011-06-28]
o DOCUMENTATION: Clarified that argument 'CT' should be tumor copy
  number ratios relative to the normal.
o DOCUMENTATION: Added Rd help for as.data.frame() of PairedPSCBS.


Version: 0.11.0 [2011-06-14]
o Renamed all column names of returned data frames such that
  they follow the camelCase naming conventions in addition
  to be somewhat shorter too.
o GENERALIZATION: Added argument 'columnNamesFlavor' to segmentByCBS().


Version: 0.10.2 [2011-06-07]
o CLEANUP: Cleaned up the example():s.
o Added more biocViews categories to DESCRIPTION


Version: 0.10.1 [2011-05-31]
o GENERALIZATION: The package can now be *installed* without the
  DNAcopy package being installed.  If package is loaded without
  DNAcopy installed, an informative message will explain how to
  install it.
o Added installDNAcopy(), which will install DNAcopy from Bioconductor.
o ROBUSTNESS: Now all DNAcopy functions are called as DNAcopy::nnn().


Version: 0.10.0 [2011-05-29]
o Renamed all arguments, variables, and functions referring to 'tau' to
  refer to 'delta' reflecting the notation of the Paired PSCBS paper.
o Renamed options, example code and help pages to reflect new package name.
o Updated references in help pages.
o Now the paired PSCBS is formally referred to as 'Paired PSCBS'.
o Renamed package to PSCBS (from 'psCBS').


Version: 0.9.54 [2011-04-27]
o Added argument 'maxC' to estimateTauLOHByMinC1ForNonAB().


Version: 0.9.53 [2011-04-14]
o Added argument 'max' to estimateTauAB() and estimateTauLOH().


Version: 0.9.52 [2011-04-14]
o BUG FIX: Argument 'minSize' of callAB() and callLOH() had no effect.


Version: 0.9.51 [2011-04-12]
o Added argument 'minSize' to callAB() and callLOH() for PairedPSCBS.
o Now the a conflicting call in callLOH()/callAB() with 
  argument xorCalls=TRUE is set to NA to contrast it from
  a FALSE call.


Version: 0.9.50 [2011-04-12]
o Added argument 'xorCalls' to callLOH() and callAB() for
  PairedPSCBS.  When TRUE (the default), a segment that 
  is already called AB will never be called LOH, and vice versa.


Version: 0.9.49 [2011-04-11]
o Updated estimateTauABBySmallDH() for PairedPSCBS to use a
  "symmetric" quantile estimator.
o Added argument 'midpoint' to estimateTauLOHByMinC1AtNonAB().
o BUG FIX: The recent callLOH() would not store the LOH calls.


Version: 0.9.48 [2011-04-10]
o Added callLOH() for PairedPSCBS, which in turn calls 
  auxillary methods.
o Added estimateTauLOH() for PairedPSCBS, which in turn calls 
  auxillary methods.
o Now callAB(..., force=FALSE) skips the caller if
  allelic-balance calls already exist.
o DOCUMENTATION: Update the exampe for segmentByPairedPSCBS
  to reflect the restructured AB and LOH callers.


Version: 0.9.47 [2011-04-08]
o Added estimateTauABBySmallDH()
o Added internal weightedQuantile().
o DOCUMENTATION: Added help pages for more methods.
o CLEANUP: Started to restructure the source code files.


Version: 0.9.46 [2011-04-08]
o BUG FIX: postsegmentTCN() for PairedPSCBS could generate an invalid
  'tcnSegRows' matrix, where the indices for two consecutive segments
  would overlap, which is invalid.  This was caught with real data,
  but it seems to have required a very rare combination of data in
  order for it to occur.


Version: 0.9.45 [2011-04-05]
o BUG FIX: estimateHighDHQuantileAtAB() for PairedPSCBS would throw
  an error on an undefined 'trim' if verbose output was used.


Version: 0.9.44 [2011-02-18]
o Added estimateHighDHQuantileAtAB() for PairedPSCBS.


Version: 0.9.43 [2011-02-06]
o BUG FIX: plotTracks2() queired non-existing argument 'tracks'.


Version: 0.9.42 [2011-02-03]
o Added estimateKappa() for estimating the normal contamination.


Version: 0.9.41 [2011-02-02]
o Updated default for 'tauAB' of callABandHighAI() and callABandLowC1()
  to be estimated from data using estimateTauAB().
o Added argument 'tauTCN' to estimateTauAB().


Version: 0.9.40 [2011-01-27]
o Added argument 'flavor' to estimateTauAB() for estimating the
  AB threshold using alternative methods.


Version: 0.9.39 [2011-01-19]
o Added trial version of new plotTracks2(), which will later replace
  plotTracks().  Currently it only works for single chromosomes.
o Added support functions, e.g. updateMeans().


Version: 0.9.38 [2011-01-18]
o DOCUMENTATION: Documented more plotTracks() arguments for PairedPSCBS.
o BUG FIX: Now plotTracks(..., add=TRUE) for PairedPSCBS plots to 
  the current figure/panel.
o Now plotTracks(..., add=FALSE) for PairedPSCBS only sets up subplots
  if argument 'tracks' specifies more than one panel.
o Added arguments 'changepoints' and 'col' to plotTracks() for PairedPSCBS.


Version: 0.9.37 [2011-01-18]
o BUG FIX: 'tcnSegRows' and 'dhSegRows' where not updated by
  extractByRegions() for PairedPSCBS.


Version: 0.9.36 [2011-01-14]
o Added estimateTauAB() for estimating the tauAB tuning parameter
  when calling segments in allelic balance.  Updated 
  example(segmentByPairedPSCBS) to illustrate how to use it.
o Added extractByRegions() for PairedPSCBS.


Version: 0.9.35 [2011-01-12]
o Now postsegmentTCN(..., force=TRUE) for PairedPSCBS also updates
  the TCN estimates even for segments where the DH segmentation did
  not find any additional change points.


Version: 0.9.34 [2010-12-09]
o BUG FIX: When there were multiple chromsomes processed by
  segmentByPairedPSCBS(), then the returned data object would
  contain 'betaT' identical to 'betaTN'.


Version: 0.9.33 [2010-12-07]
o Added callLowC1ByC1() and callABandLowC1().


Version: 0.9.32 [2010-12-03]
o BUG FIX: In rare cases the bootstrap sanity checks can indeed produce
  an invalid 'range', more precisely where (range[,2] >= range[,1]) is
  not true.  This can happen if there is no variation in the bootstrap
  estimates.  Beause of this we allow for some tolerance.


Version: 0.9.31 [2010-12-02]
o Added option "psCBS/sanityChecks/tolerance" for specifying the 
  tolerance of some internal sanity checks.  


Version: 0.9.30 [2010-12-01]
o Rewrote all code dealing with the identification of loci belong
  to segments.  The code is now utilizing the 'segRows' element
  returned by DNAcopy::segment().  Lots of the code was rewritten
  and therefore completely new bugs may have been introduced.


Version: 0.9.25 [2010-11-30]
o BUG FIX: Argument 'flavor' of segmentByPairedPSCBS() would be ignored
  if multiple chromsomomes were segmented.
o BUG FIX: extractByChromosome() for PSCBS would call it self instead
  of extractByChromosomes().


Version: 0.9.24 [2010-11-28]
o BUG FIX: postsegmentTCN() did not handle loci with the same positions
  and that are split in two different segments.  It also did not exclude
  loci with missing values.


Version: 0.9.23 [2010-11-28]
o BUG FIX: The algorithm in segmentByCBS() that infers which loci (of
  the ones share the same genomic positions) that should be exclude
  from each segment did not take missing signals into account.
o BUG FIX: Iff argument 'chromosome' to segmentByPairedPSCBS() was of
  length greater than one and specified exactly one unique chromosome,
  then exception "Number of elements in argument 'chromosome' should
  be exactly 8712 not 86209 value(s)" would be thrown.


Version: 0.9.22 [2010-11-27]
o BUG FIX: bootstrapTCNandDHByRegion() would incorrectly include
  non-polymorphic loci in the set of homozygous SNPs during resampling.
o BUG FIX: segmentByPairedPSCBS() would not accept missing values in
  argument 'chromosome'.


Version: 0.9.21 [2010-11-27]
o Now arguments '...' of segmentByPairedPSCBS() are passed to
  the two segmentByCBS() calls.
o Added callSegmentationOutliers(), which can be used to identify
  single-locus outliers that have a genomic signal that is clearly
  outside the expected range.  The dropSegmentationOutliers() sets
  locus outliers detected by this method to missing values. 
  This is useful for excluding total copy-number outliers that
  otherwise can have a dramatic impact on the non-robust CBS method.


Version: 0.9.20 [2010-11-26]
o Added optional argument 'chromosomes' to plotTracks() to plot a
  subset of all chromosomes.
o Added extractByChromosomes() for PSCBS.
o Now the default confidence intervals for plotTracks() is (0.05,0.95),
  if existing.
o Now all call functions estimate symmetric bootstrap quantiles for
  convenince of plotting confidence intervals.
o BUG FIX: callABandHighAI() for PairedPSCBS used the old DH-only
  bootstrap method.
o BUG FIX: The statistical sanity checks of the bootstrap estimates
  would give an error when only single-sided bootstrap confidence
  interval was calculated.
o BUG FIX: The call functions, for instance callABandHighAI(), would throw
  'Error in quantile.default(x, probs = alpha) : missing values and NaN's
  not allowed if 'na.rm' is FALSE' unless bootstrapTCNandDHByRegion() was
  run before.


Version: 0.9.19 [2010-11-23]
o ROBUSTNESS: Added more sanity checks to bootstrapTCNandDHByRegion().
o WORKAROUND: The precision of the mean levels of DNAcopy::segment()
  is not great enough to always compare it to that of R's estimates.
o BUG FIX: bootstrapTCNandDHByRegion() would give an error if there was
  only one segment.
o BUG FIX: segmentByPairedPSCBS() and bootstrapTCNandDHByRegion() 
  would not subset the correct set of DH signals if there were some
  missing values in TCN.


Version: 0.9.18 [2010-11-22]
o Added argument 'calls' to plotTracks() for highlighing called regions.
o Updated callAllelicBalanceByDH() and callExtremeAllelicImbalanceByDH()
  to utilize bootstrapTCNandDHByRegion().
o ROBUSTNESS: Now drawConfidenceBands() of PairedPSCBS silently does
  nothing if the requested bootstrap quantiles are available.
o BUG FIX: bootstrapTCNandDHByRegion() for PairedPSCBS would not
  correctly detect if bootstrap results are already available.


Version: 0.9.17 [2010-11-21]
o Now plotTracks() supports tracks "tcn,c1", "tcn,c2" and "c1,c2" too.
o Added support for flavor "tcn&dh" in segmentByPairedPSCBS(), which
  contrary to "tcn,dh" enforces TCN and DH to have the same change
  points.  The default flavor is now "tcn&dh".
o Added argument 'xlim' to plotTracks() making it possible to zoom in.


Version: 0.9.16 [2010-11-21]
o Now joinSegments=TRUE is the default for segmentByCBS() and
  segmentByPairedPSCBS().
o Added argument 'quantiles' to plotTracks(), which if specified
  draws confidence bands previously estimated from bootstrapping.
o Added drawConfidenceBands() for PairedPSCBS.
o Added bootstrapTCNandDHByRegion() for PairedPSCBS.
o Added standalone joinSegments() for CBS results.
o Now segmentByPairedPSCBS() also returns minor and major 
  copy numbers for each segment.


Version: 0.9.15 [2010-11-21]
o Adjusted postsegmentTCN() such that the updated TCN segment boundaries
  are the maximum of the DH segment and the support by the loci.  This
  means that postsegmentTCN() will work as expected both when signals
  where segmented with 'joinSegments' being TRUE or FALSE.
o Updated plotTracks() for PairedPSCBS such that the TCN segmentation
  is colored 'purple' and the DH segmentation 'orange' for TCH and DH
  only tracks.


Version: 0.9.14 [2010-11-20]
o Now it is possible to specify the boundaries of the regions to
  be segmented as known change points via argument 'knownCPs'.
o Added argument 'joinSegments' to segmentByCBS() and 
  segmentByPairedPSCBS() in order to specify if neighboring 
  segments should be joined or not.
o Now segmentByCBS() and segmentByPairedPSCBS() allow for 
  unknown genomic positions as well as missing total CN signals.


Version: 0.9.13 [2010-11-19]
o Added argument 'joinSegments' to segmentByCBS() in order to specify
  if neighboring segments should be joined or not.


Version: 0.9.12 [2010-11-19]
o Added plotTracks() and drawLevels() etc to CBS results.
o Now segmentByCBS() allows for unknown genomic positions.
o Now segmentByCBS() allows for missing signals.
o Added argument 'preserveOrder' to segmentByCBS().  If TRUE, then
  the loci in the returned 'data' object are ordered as the input
  data, otherwise it is ordered along the genome.


Version: 0.9.11 [2010-11-16]
o Now the 'data' object returned by segmentByCBS() contains field
  'index' if and only if the loci had to be reorder along the genome.
o DOCUMENTATION: Added more details, references to papers, and cross
  links to other functions to the help pages.
o BUG FIX: In the rare cases where two loci at the same positions are
  split up into two neighboring segments, then segmentByPairedPSCBS()
  would fail to infer which they were if and only if the loci were not
  ordered along the genome.  This could happen with for instance
  Affymetrix GenomeWideSNP_6 data.


Version: 0.9.10 [2010-11-09]
o Added argument 'cex=1' to plotTracks().
o BUG FIX: It was not possible to plot BAF tracks with plotTracks().


Version: 0.9.9 [2010-11-05]
o BUG FIX: segmentByCBS() tried to pass non-existing argument
  'undo.split' to DNAcopy::segment().  It should be 'undo.splits'.


Version: 0.9.8 [2010-11-04]
o BUG FIX: There was a stray/debug stop() statement left in  
  segmentByPairedPSCBS() causing an "error" in the rare case 
  when loci that have the same physical locations are split
  into two different segments.


Version: 0.9.7 [2010-11-03]
o ROBUSTNESS: Now bootstrapDHByRegion() uses resample() of R.utils.
o BUG FIX: bootstrapDHByRegion() did not sample from the correct
  unit(s) when there was only one DH signal.


Version: 0.9.6 [2010-11-02]
o Added arguments 'undoTCN' and 'undoDH' to segmentByPairedPSCBS().
o Added argument 'undo' to segmentByCBS(), which corresponds to
  undo.splits="sdundo" and undo.SD=undo, if undo < +Inf.
o BUG FIX: Arguments 'alphaTCN' and 'alphaDH' of segmentByPairedPSCBS()
  were not used when more than one chromosome were segmented.


Version: 0.9.5 [2010-11-01]
o Added arguments 'alphaAB' and 'alphaHighAI' to callABandHighAI().
o BUG FIX: bootstrapDHByRegion() would give an error if only a single
  quantile was requested.
o BUG FIX: bootstrapDHByRegion() would give "Error in if (nbrOfUnits
  > segJJ[, "dh.num.mark"]) { : missing value where TRUE/FALSE needed"
  when 'dh.num.mark' was NA.


Version: 0.9.4 [2010-10-25]
o Now the default is a 95% confidence interval for calls.
o Now segmentByCBS() also returns element 'lociNotPartOfSegment',
  if there are segments that share end points, which can happen if
  a change point is called in middle of a set of loci that have the
  same genomic positions.  In such cases, 'lociNotPartOfSegment'
  specifies which loci are *not* part of which segment.  Then by
  identifying the loci that are within a segment by their positions
  and excluding any of the above, one knows exactly which loci
  CBS included in each segment.
o BUG FIX: Now bootstrapDHByRegion() for PairedPSCBS handles the
  rare case when markers with the same positions are split in 
  two different segments.
o BUG FIX: Now the correct set of loci are extracted from each TCN
  segment, in the rare case that two neighboring TCN segments have
  the same end points.


Version: 0.9.3 [2010-10-25]
o Added argument 'ciRange' to callAllelicBalance() and
  callExtremeAllelicImbalance().
o BUG FIX: bootstrapDHByRegion() for PairedPSCBS would bootstrap 
  from the incorrect set of loci when the DH region contained 
  only one locus.
o BUG FIX: bootstrapDHByRegion() for PairedPSCBS would bootstrap 
  from the incorrect set of loci if more than one chromosome 
  was available.


Version: 0.9.2 [2010-10-24]
o BUG FIX: plotTracks() would give "Error: object 'nbrOfLoci' not found'
  for whole-genome plots.


Version: 0.9.1 [2010-10-20]
o Now plotTracks() can plot whole-genome data.


Version: 0.9.0 [2010-10-18]
o Added arguments 'alphaTCN' and 'alphaDH' to segmentByPairedPSCBS()
  with defaults according to the paper.


Version: 0.8.3 [2010-10-18]
o Now segmentByPairedPSCBS() can segment multiple chromosomes.


Version: 0.8.2 [2010-10-17]
o Added argument 'tbn' to segmentByPairedPSCBS() specifying whether
  TumorBoostNormalization should be applied or not.


Version: 0.8.1 [2010-10-10]
o The default for segmentByPairedPSCBS() is now to segment TCN on
  the original scale, not the sqrt().
o Added plotTracks() for PairedPSCBS.


Version: 0.8.0 [2010-10-06]
o CLEAN UP: Removed all old code, native code and help pages.


Version: 0.7.8 [2010-10-03]
o Added optional argument 'chromosome' to segmentByCBS().
  Note that at this point it is only used for annotating the
  results; it can not be used to segmented multiple chromosomes
  at ones.


Version: 0.7.7 [2010-09-26]
o Now subsetBySegments() and postsegmentTCN() for PairedPSCBS 
  handles multiple chromosomes.


Version: 0.7.6 [2010-09-24]
o Added support to annotating and subsetting also by chromosomes,
  as well as appending segmentation results from different chromosomes
  together.


Version: 0.7.5 [2010-09-21]
o Added postsegmentTCN() for PairedPSCBS, which updates the 
  TCN segment start and ends, estimates and counts given the
  DH segments.


Version: 0.7.4 [2010-09-18]
o Added argument 'chromosome' to segmentByPairedPSCBS(), which, if given,
  adds a chromosome column to the data and segmentation results.
o BUG FIX: plot() for PairedPSCBS used a non-defined variable.


Version: 0.7.3 [2010-09-16]
o Added callABandHighAI() for calling paired PSCBS segmentation results.
o Added internal bootstrapping functions.


Version: 0.7.2 [2010-09-15]
o Added more methods for the PSCBS class.


Version: 0.7.1 [2010-09-08]
o Added more methods for the PSCBS class.
o Now segmentByPairedPSCBS() also returns the TumorBoost normalized data.


Version: 0.7.0 [2010-09-04]
o Updated segmentByPairedPSCBS() to provide two-step segmentation 
  from first segmenting the total copy numbers and then the
  decrease-of-heterozygosity signals.  Added utility functions for
  plotting the results.  The code for calling allelic imbalance
  and LOH is still to be added.


Version: 0.6.3 [2010-09-02]
o ROBUSTNESS: Now segmentByCBS() also works if there are no data points.


Version: 0.6.2 [2010-07-14]
o CLEAN UP: Added callNaiveHeterzygotes() which is a cleaned up
  version of findheterozygous().  Added an Rd example that asserts
  that the two are identical and compares the calls to those of
  aroma.light::callNaiveGenotypes().


Version: 0.6.1 [2010-07-09]
o Added low-level segmentByPairedPSCBS(), which runs paired PSCBS
  segmentation on a single sample and a single chromosome.
  It only segments; it does not call segments.  This is only
  a stub in the sense that it still does not adjust p-values etc.
o Added low-level segmentByCBS(), which runs CBS segmentation
  on a single sample and a single chromosome.
o BACKWARD COMPATIBILITY: Now psCNA() returns a list of length 8.
o Reverted psSegment() back to v0.5.6.


Version: 0.6.0 [2010-07-08]
o Now psSegmentPaired() returns a data frame (no longer a matrix).
o CLEANUP: Major cleanup, i.e. renaming variables, reordering etc.
o CLEANUP: Created psSegmentPaired() from psSegment().
o ROBUSTNESS: Replaced all 1:n with seq(length=n) to deal with n == 0.
o ROBUSTNESS: Now all list elements are referenced by name.
o ROBUSTNESS: Now all iterator variables are written as ii, jj etc.
o Using setMethodS3() of R.methodsS3 to define S3 method.
o Dropping NAMESPACE while package is finished.  This makes it
  easier to patch methods etc.


Version: 0.5.6 [2010-07-07]
o Added example(psSegment).
o BUG FIX: Previous clean up introduced bugs.
o BUG FIX: The dynamic library for hrmode() was not loaded.


Version: 0.5.5 [2010-05-05]
o CLEAN UP/ROBUSTNESS: Major code clean up.


Version: 0.5.4 [2010-04-30]
o Added internal hrmode().
o CLEAN UP: Renamed source files to match function names.
  Only only function per source file.


Version: 0.5.3 [2010-04-22]
o ABO updated the psCBS algorithm.


Version: 0.5.2 [2010-0?-??]
o ???


Version: 0.5.1 [2010-03-31]
o Now psSegment(..., matching.reference=TRUE) does TumorBoost 
  normalization on the allele B fractions before segmentation.


Version: 0.5.0 [2010-03-12]
o Added to R-forge repository.