Annotated Copy-Number Regions

Provides SNP array data from different types of copy-number regions. These regions were identified manually by the authors of the package and may be used to generate realistic data sets with known truth.


This data package contains SNP array data from different platforms (Affymetrix and Immumina) and different types of copy-number regions. These regions were identified manually by the authors of the package and may be used to generate realistic data sets with known truth.

Currently the acnr package contains three data sets curated from GEO: > listDataSets() [1] "GSE11976_CRL2324" "GSE13372_HCC1143" "GSE29172_H1395"

This package was initially built to serve as a data package for the jointseg package.

Software status

Resource: CRAN Travis CI Appveyor
Platforms: Multiple Linux & OS X Windows
R CMD check CRAN version Build status
Test coverage Coverage Status

News

acnr 1.0.0 [2017-04-15]

  • Updated data set GSE29172_H1395 by taking only the first 5000 loci of each region in order to maintain package size <3Mb.
  • Added inst/CITATION.
  • Minor updates to doc.

acnr 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.

acnr 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).

acnr 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.

acnr 0.2.8 [2016-11-25]

  • Added functions 'listDataSets' and 'listTumorFractions'

acnr 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

acnr 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)

acnr 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

acnr 0.2.4 [2014-11-17]

  • Used tools::resaveRdaFiles to compress data

acnr 0.2.3 [2014-10-27]

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

acnr 0.2.2 [2014-09-08]

  • Added a mini-vignette.

acnr 0.2.1 [2014-05-30]

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

acnr 0.2.0 [2014-05-30]

  • Changed ‘platform’ to ‘dataSet’.

acnr 0.1.7 [2014-05-27]

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

acnr 0.1.6 [2014-05-14]

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

acnr 0.1.5 [2014-02-20]

  • Added a succinct vignette.

acnr 0.1.4 [2013-12-04]

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

acnr 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.

acnr 0.1.2 [2013-03-15]

  • Added more regions for Illumina platform

acnr 0.1.1 [2013-02-07]

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

acnr 0.1.0 [2013-01-31]

  • Created from package 'jointSeg'.

Reference manual

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install.packages("acnr")

1.0.0 by Morgane Pierre-Jean, 2 years ago


https://github.com/mpierrejean/acnr


Report a bug at https://github.com/mpierrejean/acnr/issues


Browse source code at https://github.com/cran/acnr


Authors: Morgane Pierre-Jean [aut, cre] , Pierre Neuvial [aut]


Documentation:   PDF Manual  


LGPL (>= 2.1) license


Suggests R.utils, knitr, rmarkdown, testthat


Imported by jointseg.


See at CRAN