acnr: Annotated Copy-Number Regions
Version 1.0.0

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.

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
URL https://github.com/mpierrejean/acnr
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("acnr")

Getting started

Package overview
README.md
Annotated data sets contained in the `acnr` package
Autocorrelation plots

Popular man pages

acnr-package: Annotated Copy-Number Regions
getMinorMajorCopyNumbers: Get minor and major copy number labels from region annotation...
GSE13372_HCC1143: Annotated copy-number regions from the GEO GSE13372 data set.
GSE29172_H1395: Annotated copy-number regions from the GEO GSE29172 (and...
listDataSets: List available data sets
listTumorFractions: List of available tumor fractions for a data set
loadCnRegionData: loadCnRegionData
See all...

All man pages Function index File listing

Man pages

acnr-package: Annotated Copy-Number Regions
getMinorMajorCopyNumbers: Get minor and major copy number labels from region annotation...
GSE11976_CRL2324: Annotated copy-number regions from the GEO GSE11976 data set.
GSE13372_HCC1143: Annotated copy-number regions from the GEO GSE13372 data set.
GSE29172_H1395: Annotated copy-number regions from the GEO GSE29172 (and...
listDataSets: List available data sets
listTumorFractions: List of available tumor fractions for a data set
loadCnRegionData: loadCnRegionData

Functions

GSE11976_CRL2324 Man page
GSE13372_HCC1143 Man page
GSE29172_H1395 Man page
acnr Man page
acnr-package Man page
getMinorMajorCopyNumbers Man page Source code
listDataSets Man page Source code
listTumorFractions Man page Source code
loadCnRegionData Man page Source code
loadDataSet Source code

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
acnr documentation built on May 19, 2017, 10:27 p.m.

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