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NEWS.md

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Package: acnr

Version: 0.3.2 [2017-01-06]

  • Updated data set GSE13372_HCC1143 to make all regions have a comparable number of data points (0,2) was ~7x bigger than the other ones.

Version: 0.3.1 [2017-01-05]

  • BUG FIX in data set GSE13372_HCC1143: tumor genotypes were mislabeled as normal (Issue #9)
  • BUG FIX in data set GSE11976_CRL2324: genotypes were in 0, 1, 2 instead of 0, 1/2, 1.
  • Added a test to check the consistency of germline genotypes.
  • Added other tests to check the internal consistency of all data sets (colum names, germline data, region annotation) to address Issues #6 and #8.
  • Removed tumor fractions 0.23, 0.45, and 0.47 for which the cellularity is clearly inconsistent with experimental results, see Table 3 in Staaf (2008).

Version: 0.3.0 [2016-12-15]

  • Data sets are now stored in inst/extData.
  • Data sets are now documented individually.
  • Updated scripts for the preprocessing of data set GSE13372.
  • Now exporting 'betaT' and 'betaN' for data set GSE13372.
  • 12 tumor cellularities are now available for data set GSE11976.

Version: 0.2.8 [2016-11-25]

  • Added functions 'listDataSets' and 'listTumorFractions'

Version: 0.2.7 [2016-11-24]

  • Updated scripts for the preprocessing of data set GSE29172
  • Now exporting 'betaT' and 'betaN' for data set GSE29172
  • Renamed files from Affymetrix data sets

Version: 0.2.6 [2016-11-23]

  • Moved to roxygen2 documentation using package 'Rd2roxygen'
  • Cleaned up DESCRIPTOIN
  • Passes R CMD check locally with one NOTE (long file paths)

Version: 0.2.5 [2016-05-04]

  • Add a new dataSet GSE13372
  • Change directory structure in inst/exdata: now inst/exdata/dataSet/chipType
  • Save all files in '.rds'
  • Add a 0% dillution in 'GSE11976' dataset

Version: 0.2.4 [2014-11-17]

  • Used tools::resaveRdaFiles to compress data

Version: 0.2.3 [2014-10-27]

  • Changed ‘Affymetrix’ data, package is now less than 5MB.

Version: 0.2.2 [2014-09-08]

  • Added a mini-vignette.

Version: 0.2.1 [2014-05-30]

  • Moved inst/testScripts/system/preprocessing to inst/preprocessing.

Version: 0.2.0 [2014-05-30]

  • Changed ‘platform’ to ‘dataSet’.

Version: 0.1.7 [2014-05-27]

  • Changed ‘Illumina’ to ‘GSE11976’ and ‘Affymetrix’ to ‘GSE29172’.

Version: 0.1.6 [2014-05-14]

  • Bumped up version number to trigger build of 'jointSeg' by R-forge.

Version: 0.1.5 [2014-02-20]

  • Added a succinct vignette.

Version: 0.1.4 [2013-12-04]

  • Changed (1,2) region in Illumina Data.

Version: 0.1.3 [2013-04-13]

  • Now 'c' is on the non-log scale for both Affy and Illumina.
  • In 'loadCnRegionData': more informative error message when desired tumor fraction is not available.

Version: 0.1.2 [2013-03-15]

  • Added more regions for Illumina platform

Version: 0.1.1 [2013-02-07]

  • Renamed 'inst/extData' to 'inst/extdata'

Version: 0.1.0 [2013-01-31]

  • Created from package 'jointSeg'.