Package: aroma.tcga
===================

Version: 0.5.3 (2010-04-05)
o Updated scripts so that data from jhu-usc.edu (DNA methylation) 
  and unc.edu (gene and miRNA expression) can be downloaded.


Version: 0.5.2 (2010-04-04)
o Increased the package dependency requirements.


Version: 0.5.1 (2010-03-08)
o BUG FIX: exportGenotypeCallsAndConfidenceScores() for class
  BroadBirdseedGenotypeTcgaDataFile could give the error message
  "object 'naValue' not found".


Version: 0.5.0 (2010-03-02)
o Updates scripts so that download of Harvard CN files works again.


Version: 0.4.2 (2010-01-18)
o Added a ASCRMAv2 script.
o Started to update code and scripts to also recognize archives
  in the new DCC v3 format.  Still lots to add, e.g. MD5 file 
  checksum validation of downloads etc.


Version: 0.4.1 (2010-01-08)
o Added extractTumorNormalPairs() for GenericDataFileSet.


Version: 0.4.0 (2010-01-07)
o Added static readBCRSamplesTable() of TcgaDccDownloader for
  downloading the BCR sample HTML table, converting it to a
  tab-delimited text file, and returning it as a data frame. 


Version: 0.3.3 (2010-01-07)
o SCRIPTS: Added script to import ASCRMAv2 chip-effect sets.
o SCRIPTS: The testScripts/system/ now have more informative names, 
  and are more convenient in interactive mode.
o Added argument 'samplePatterns' to exportTotalAndFracB() for
  HudsonAlphaXYTcgaDataFile, which can be used to export a subset of
  the data for particular TCGA samples.
o BUG FIX: Forgot to assign default NAs to allocated files.  Updated
  aroma.core v1.4.1 to assign NAs by default.


Version: 0.3.2 (2010-01-06)
o Added extractByTcgaType() for GenericDataFileSet.  It asserts
  that the names of the files in the data set are valid TCGA names.
o Added default maxNbrOfUnknownUnitNames=0 to all exportNnn() function.


Version: 0.3.1 (2010-01-05)
o Added BroadAfter5NNTotalCopyNumberTcgaDataFile to match
  *.after_5NN.copynumber.data.txt files.  The former one
  BroadTotalCopyNumberTcgaDataFile now matches only
  *.copynumber.data.txt files (not including the above).
o WORKAROUND: Added getColumnNames() for MskccTotalCopyNumberTcgaDataFile 
  that detects empty column names and replaces them with a default name.
o WORKAROUND: Some of the TCGA data files are not MAGE-TAB files,
  but rather regular tab-delimited files.  Updated getHeader() of 
  MageTabDataMatrixFile to detect this.


Version: 0.3.0 (2010-01-04)
o Added MskccTotalCopyNumberTcgaData(File|FileSet).
o Added HarvardTotalCopyNumberTcgaData(File|FileSet).
o Added getDefaultFullName(... parent=1) to TcgaDataFileSet so that 
  it handles the updated ditto in R.filesets (now with parent=0).
o ROBUSTNESS: Updated getKnownFilePatterns() of TcgaDccDownloader to
  "^(^.)+(.)copynumber(.)data(.)txt$" in order to avoid getting 
  "(.)no_outlier(.)copynumber(.)data(.)txt$" files too.
o BUG FIX: exportTotalAndFracB(..., force=FALSE) for
  BroadTotalCopyNumberTcgaDataFile would never export.


Version: 0.2.5 (2010-01-01)
o ROBUSTNESS: Using new Arguments$getInstanceOf() were possible.


Version: 0.2.4 (2009-12-05)
o Added HudsonAlphaGenotypeTcgaDataFile(Set) with exportTotalCalls().
o BUG FIX: exportTotalAndFracB() of HudsonAlphaBAlleleFreqTcgaDataFile
  would not export data unless force=TRUE.


Version: 0.2.3 (2009-11-06)
o Added HudsonAlphaXYTcgaDataFile|Set classes.


Version: 0.2.2 (2009-11-02)
o Added exportGenotypeCallsAndConfidenceScores() to
  BroadBirdseedGenotypeTcgaDataFileSet.


Version: 0.2.1 (2009-11-02)
o Added HudsonAlphaBAlleleFreqTcgaDataFile|Set classes.


Version: 0.2.0 (2009-11-01)
o Updated dependencies.


Version: 0.1.8 (2009-10-30)
o Added exportTotalAndFracB() for BroadTotalCopyNumberTcgaDataFile
  and BroadTotalCopyNumberTcgaDataFileSet.
o Now makeFullNamesTranslator() of SdrfFile|Set adds a "failTag" 
  to the fullname of those fullnames that was not translated.
o BUG FIX: getBarcodeIdTranslators() of TcgaFullNameTranslators 
  would drop fullnames that did not match the pattern.


Version: 0.1.7 (2009-10-29)
o Added default argument 'ignore.case=TRUE' to listFiles(...)
  of TcgaDccDownloader.
o Added exportGenotypeCallsAndConfidenceScores() to
  BroadBirdseedGenotypeTcgaDataFile.


Version: 0.1.6 (2009-10-25)
o Added BroadBirdseedGenotypeTcgaData(File|FileSet).
o Added *FileSet classes for all *File classes.


Version: 0.1.5 (2009-10-23)
o OPTIMIZATION: Now makeFullNamesTranslator() of SdrfFileSet caches the
  result in the memory so it does not have to reread the files each times.
o Added appendFullNameTranslatorBySdrfFile{Set}() for FullNameInterface.
  Dropped ditto for GenericDataFileSet.


Version: 0.1.4 (2009-10-22)
o Added TcgaFullNameTranslators.
o Added argument 'onError' to downloadFile().
o Added argument 'order' to downloadFilesByPattern().
o Renamed downloadFiles() to downloadFilesByPattern().
o Now downloadFile() only download files available in the MANIFEST file.
o Added hasFiles() and hasFile() to TcgaDccDownloader. 
o Added getKnownFilePatterns() to TcgaDccDownloader.  The information
  is currently hardwired in the source code but should be handled by
  customable data files.


Version: 0.1.3 (2009-10-20)
o Added static findDataSets() to TcgaDccData.


Version: 0.1.2 (2009-10-16)
o Stricter dependencies.


Version: 0.1.1 (2009-10-02)
o Added makeFullNamesTranslator() to SdrfFile and SdrfFileSet.
o Added setFullNamesTranslatorBySdrfFile() to GenericDataFileSet.
o Added the SdrfFileSet class.


Version: 0.1.0 (2009-09-25)
o Added testScripts/.


Version: 0.0.9 (2009-09-24)
p Added BroadTotalCopyNumberTcgaDataFile.
o Added argument 'strict=FALSE' to getHeader() of MageTabDataMatrixFile.
  If FALSE, empty "Hybridization REF" fields are removed.  This is
  a workaround in order to read *.after_5NN.copynumber.data data files
  from the Broad Institute.


Version: 0.0.8 (2009-08-26)
o Added BroadAlleleSpecificThetaTcgaDataFile.
o Added BroadAlleleSpecificCopyNumberTcgaDataFile.
o Added TcgaDataFile.


Version: 0.0.7 (2009-08-20)
o Now getHeader() of MageTabDataMatrixFile also recognizes columns 
  named '(Rtum/Rnorm)'.


Version: 0.0.6 (2009-05-22)
o Added SdrfFile.


Version: 0.0.5 (2009-05-18)
o Added MageTabFile and MageTabDataMatrixFile classes.


Version: 0.0.4 (2009-04-18)


Version: 0.0.3 (2009-04-16)
o Added downloadFiles() to TcgaDccDownloader.
o Added setLogin() to TcgaDccDownloader.
o BUG FIX: Root path was tgcaData/ (not tcgaData/).


Version: 0.0.2 (2009-04-13)
o Now tested for both public and protected data set.


Version: 0.0.1 (2009-04-07)
o Created.
