NEWS

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acnr 0.3.2

• 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.

acnr 0.3.1

• 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).

acnr 0.3.0

• 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.

acnr 0.2.8

• Added functions 'listDataSets' and 'listTumorFractions'

acnr 0.2.7

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

acnr 0.2.6

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

acnr 0.2.5

• 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

acnr 0.2.4 (2014-11-19)

• Used tools::resaveRdaFiles to compress data

acnr 0.2.3

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

acnr 0.2.2

• Added a mini-vignette.

acnr 0.2.1

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

acnr 0.2.0

• Changed ‘platform’ to ‘dataSet’.

acnr 0.1.7

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

acnr 0.1.6

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

acnr 0.1.5

• Added a succinct vignette.

acnr 0.1.4

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

acnr 0.1.3

• 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.

acnr 0.1.2

• Added more regions for Illumina platform

acnr 0.1.1

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

acnr 0.1.0

• Created from package 'jointSeg'.