acnr: 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.

Install the latest version of this package by entering the following in R:
install.packages("acnr")
AuthorMorgane Pierre-Jean [aut, cre], Pierre Neuvial [aut]
Date of publication2017-04-18 09:58:15 UTC
MaintainerMorgane Pierre-Jean <morgane.pierrejean@genopole.cnrs.fr>
LicenseLGPL (>= 2.1)
Version1.0.0
https://github.com/mpierrejean/acnr

View on CRAN

Files

inst
inst/CITATION
inst/preprocessing
inst/preprocessing/GSE29172
inst/preprocessing/GSE29172/07.exportRegionData.R inst/preprocessing/GSE29172/00.install.R inst/preprocessing/GSE29172/02.doASCRMAv2.R inst/preprocessing/GSE29172/01.checkAnnotationData.R inst/preprocessing/GSE29172/05.defineCopyNumberSegments.R inst/preprocessing/GSE29172/06.plotCopyNumberSegments.R inst/preprocessing/GSE29172/09.LightCnRegionData.R inst/preprocessing/GSE29172/03.writeWholeGenomeData.R inst/preprocessing/GSE29172/08.mergeCnRegionData.R inst/preprocessing/GSE29172/04.plotTracks.R
inst/preprocessing/GSE11976
inst/preprocessing/GSE11976/02.exportRegionData.R inst/preprocessing/GSE11976/01.defineCopyNumberSegments.R inst/preprocessing/GSE11976/03.mergeCnRegionData.R inst/preprocessing/GSE11976/00.PrepareData.R inst/preprocessing/GSE11976/03.plotRegions.R
inst/preprocessing/GSE13372
inst/preprocessing/GSE13372/06.exportRegionData.R inst/preprocessing/GSE13372/00.install.R inst/preprocessing/GSE13372/07.mergeCnRegionData.R inst/preprocessing/GSE13372/01.downloadAnnotationData.R inst/preprocessing/GSE13372/01.checkAnnotationData.R inst/preprocessing/GSE13372/05.defineCopyNumberSegments.R inst/preprocessing/GSE13372/03.doASCRMAv2.R inst/preprocessing/GSE13372/04.writeWholeGenomeData.R inst/preprocessing/GSE13372/02.downloadRawData.R
inst/extdata
inst/extdata/GSE29172_H1395.rds
inst/extdata/GSE13372_HCC1143.rds
inst/extdata/GSE11976_CRL2324.rds
inst/doc
inst/doc/acnr.html
inst/doc/autocorrelation.R
inst/doc/autocorrelation.html
inst/doc/acnr.R
inst/doc/autocorrelation.Rmd
inst/doc/acnr.Rmd
tests
tests/testthat.R
tests/testthat
tests/testthat/test_tumorFractions.R tests/testthat/test_monotonicCopyNumbers.R tests/testthat/test_dataSetConsistency.R tests/testthat/test_germlineGenotypes.R
NAMESPACE
NEWS.md
R
R/loadDataSet.R R/listDataSets.R R/extdata.R R/loadCnRegionData.R R/listTumorFractions.R R/getMinorMajorCopyNumbers.R
vignettes
vignettes/autocorrelation.Rmd
vignettes/acnr.Rmd
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/listDataSets.Rd man/getMinorMajorCopyNumbers.Rd man/GSE11976_CRL2324.Rd man/listTumorFractions.Rd man/GSE29172_H1395.Rd man/GSE13372_HCC1143.Rd man/acnr-package.Rd man/loadCnRegionData.Rd

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