aroma.cn: Copy-Number Analysis of Large Microarray Data Sets

Methods for analyzing DNA copy-number data. Specifically, this package implements the multi-source copy-number normalization (MSCN) method for normalizing copy-number data obtained on various platforms and technologies. It also implements the TumorBoost method for normalizing paired tumor-normal SNP data.

Author
Henrik Bengtsson [aut, cre, cph], Pierre Neuvial [aut]
Date of publication
2015-10-28 00:08:16
Maintainer
Henrik Bengtsson <henrikb@braju.com>
License
LGPL (>= 2.1)
Version
1.6.1
URLs

View on CRAN

Man pages

AbstractCurveNormalization
The AbstractCurveNormalization class
aroma.cn-package
Package aroma.cn
callAllelicBalanceByBAFs.PairedPSCBS
Calls regions that are in allelic balance
callCopyNeutralRegions.PairedPSCBS
Calls regions that are copy neutral
callPeaks.PeaksAndValleys
Calls the peaks in peaks-and-valley estimates
callXXorXY.numeric
Calls XX or XY from ChrX allele B fractions of a normal...
cnr
Simple creation of a CopyNumberRegions object
extractTupleOfDataFiles.MultiSourceCopyNumberNormalization
Gets a list of data files for a particular name across...
findAtomicAberrations.CopyNumberRegions
Finds all possible atomic regions
fitOne.MultiSourceCopyNumberNormalization
Fits the multi-source model for one sample
getAllNames.MultiSourceCopyNumberNormalization
Gets the names of all unique samples across all sources
getFitAromaUgpFile.MultiSourceCopyNumberNormalization
Gets the UGP file specifying the common set of loci to...
getInputDataSets.MultiSourceCopyNumberNormalization
Gets the list of data sets to be normalized
getSmoothedDataSets.MultiSourceCopyNumberNormalization
Gets the data sets smoothed toward the UGP file
getSubsetToFit.MultiSourceCopyNumberNormalization
Gets subset of (smoothing) units for fitting the model
MultiSourceCopyNumberNormalization
The MultiSourceCopyNumberNormalization class
Non-documented_objects
Non-documented objects
normalizeBAFsByRegions.PairedPSCBS
Normalizes allele B fractions (BAFs) based on region-based...
normalizeMirroredBAFsByRegions.matrix
Normalizes region-level mirrored allele B fractions (mBAFs)
normalizePrincipalCurve.matrix
Normalizes data in K dimensions using principal curves
PairedPscbsModel
The PairedPscbsModel class
PrincipalCurveNormalization
The PrincipalCurveNormalization class
process.MultiSourceCopyNumberNormalization
Normalizes all samples
testAllelicBalanceByBAFs
Tests for allelic balance in a genomic region
TotalCnBinnedSmoothing
The TotalCnBinnedSmoothing class
TotalCnKernelSmoothing
The TotalCnKernelSmoothing class
TotalCnSmoothing
The abstract TotalCnSmoothing class
TumorBoostNormalization
The TumorBoostNormalization class
XYCurveNormalization
The XYCurveNormalization class

Files in this package

aroma.cn
aroma.cn/inst
aroma.cn/inst/CITATION
aroma.cn/inst/testScripts
aroma.cn/inst/testScripts/setup
aroma.cn/inst/testScripts/setup/01c.installAllPackages.R
aroma.cn/inst/testScripts/setup/spawnTests.sh
aroma.cn/inst/testScripts/setup/99a.cleanupRootDirectories.R
aroma.cn/inst/testScripts/setup/01a.downloadAllAnnotationData.R
aroma.cn/inst/testScripts/setup/01b.downloadAllRawDataSet.R
aroma.cn/inst/testScripts/devel
aroma.cn/inst/testScripts/devel/C1C2
aroma.cn/inst/testScripts/devel/C1C2/21.PairedPSCBS,deShear,report.R
aroma.cn/inst/testScripts/devel/C1C2/31.PairedPSCBS,DP,deShear.R
aroma.cn/inst/testScripts/system
aroma.cn/inst/testScripts/system/CopyNumberProfiles
aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100909a,findAtomicAberrations.Rex
aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100911a,TumorClonality.Rex
aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100911b,TumorClonality,lineage.Rex
aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100909b,NormalContamination.Rex
aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100912b,Saturation.Rex
aroma.cn/inst/testScripts/system/CopyNumberProfiles/20100912a,SegmentationStdError.Rex
aroma.cn/inst/testScripts/system/segmentation
aroma.cn/inst/testScripts/system/segmentation/20091110,CBS.Rex
aroma.cn/inst/testScripts/system/MSLHN
aroma.cn/inst/testScripts/system/MSLHN/20091218,TCGA,MSLHCN.Rex
aroma.cn/inst/testScripts/system/pairedPSCN
aroma.cn/inst/testScripts/system/pairedPSCN/R
aroma.cn/inst/testScripts/system/pairedPSCN/R/loadAllDataSets.R
aroma.cn/inst/testScripts/system/pairedPSCN/R/00.setup.R
aroma.cn/inst/testScripts/system/pairedPSCN/R/getTumorNormalPairs.R
aroma.cn/inst/testScripts/system/pairedPSCN/R/zzz.R
aroma.cn/inst/testScripts/system/pairedPSCN/genomicPlots.tex.rsp
aroma.cn/inst/testScripts/system/CurveNormalization,OV
aroma.cn/inst/testScripts/system/CurveNormalization,OV/test20090715a,waves.Rex
aroma.cn/inst/testScripts/system/tracks
aroma.cn/inst/testScripts/system/tracks/20091008,HCC1143,CRMAv2-dChip-GTC,plot.Rex
aroma.cn/inst/testScripts/system/tracks/utils.R
aroma.cn/inst/testScripts/system/tracks/20091010,TCGA,plot.Rex
aroma.cn/inst/testScripts/system/TumorBoost
aroma.cn/inst/testScripts/system/TumorBoost/test20090429b,TBN.Rex
aroma.cn/inst/testScripts/system/TumorBoost/test20090429c,TBN,plot.Rex
aroma.cn/inst/testScripts/system/TumorBoost/test20090429d,TBN,LOH,plot.Rex
aroma.cn/inst/testScripts/system/TumorBoost/test20090429a,NGC.Rex
aroma.cn/inst/testScripts/system/TumorBoost/test20090620a,NGC.Rex
aroma.cn/inst/testScripts/system/MultiPlatform
aroma.cn/inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,shifts.Rex
aroma.cn/inst/testScripts/system/MultiPlatform/test20090209,TCGA,plot.Rex
aroma.cn/inst/testScripts/system/MultiPlatform/test20090210,TCGA,MSCN,plot.Rex
aroma.cn/inst/testScripts/system/MultiPlatform/test20090208,TCGA,MSCN.Rex
aroma.cn/inst/testScripts/system/MultiPlatform/test20100102,TCGA,MSCN,mpCBS.Rex
aroma.cn/inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,weights.Rex
aroma.cn/inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,wCBS.Rex
aroma.cn/inst/testScripts/system/MultiPlatform/test20090720,TCGA,MSCN,tracks.Rex
aroma.cn/inst/testScripts/system/CondSegmentation
aroma.cn/inst/testScripts/system/CondSegmentation/test20090927,TBN,plot.Rex
aroma.cn/inst/testScripts/system/CondSegmentation/test20091014,TBN,plot.Rex
aroma.cn/inst/testScripts/system/chipTypes
aroma.cn/inst/testScripts/system/chipTypes/GenomeWideSNP_6
aroma.cn/inst/testScripts/system/chipTypes/GenomeWideSNP_6/normalizeLoess2D.PairedPSCBS.Rex
aroma.cn/inst/testScripts/system/chipTypes/GenomeWideSNP_6/calibrateC1C2.PairedPSCBS.Rex
aroma.cn/inst/testScripts/system/chipTypes/GenomeWideSNP_6/calibrateC1C2,20111026.Rex
aroma.cn/inst/testScripts/system/chipTypes/GenomeWideSNP_6/deShearC1C2.PairedPSCBS.Rex
aroma.cn/inst/testScripts/system/chipTypes/GenomeWideSNP_6/orthogonalizeC1C2.PairedPSCBS.Rex
aroma.cn/inst/templates
aroma.cn/inst/templates/rsp
aroma.cn/inst/templates/rsp/PairedPSCBS,deShear,report.tex.rsp
aroma.cn/inst/templates/rsp/natbib.bst
aroma.cn/inst/templates/rsp/bioinformatics-journals-abbr.bib
aroma.cn/tests
aroma.cn/tests/callAllelicBalanceByBAFs.PairedPSCBS.R
aroma.cn/tests/cnr.R
aroma.cn/NAMESPACE
aroma.cn/NEWS
aroma.cn/R
aroma.cn/R/principal.curve.pairs2.R
aroma.cn/R/NaiveFracBGenotyping.R
aroma.cn/R/CopyNumberRegions.findAtomicAberrations.R
aroma.cn/R/021.dynamic_imports.R
aroma.cn/R/TotalCnSmoothing.R
aroma.cn/R/XYCurveNormalization.R
aroma.cn/R/000.R
aroma.cn/R/normalizePrincipalCurve.matrix.R
aroma.cn/R/SnpData.R
aroma.cn/R/PrincipalCurve.XTRAS.R
aroma.cn/R/PairedPSCBS.PLOT3.R
aroma.cn/R/CartesianSnpData.R
aroma.cn/R/TotalCnKernelSmoothing.R
aroma.cn/R/PairedPSCBS.backgroundCorrect.R
aroma.cn/R/TumorBoostNormalization.R
aroma.cn/R/PairedPscbsModel.R
aroma.cn/R/AromaUnitPscnBinarySet.doSegmentByPairedPSCBS.R
aroma.cn/R/999.DEPRECATED.R
aroma.cn/R/RawGenotypeCalls.R
aroma.cn/R/PairedPSCBS.BOOT.R
aroma.cn/R/009.setup.R
aroma.cn/R/PairedPSCBS.fitC1C2Peaks.R
aroma.cn/R/PruneCNA.PLOT.R
aroma.cn/R/MultiSourceCopyNumberNormalization.R
aroma.cn/R/PruneCNA.EXTS.R
aroma.cn/R/TotalCnBinnedSmoothing.R
aroma.cn/R/PairedPscbsCaller.R
aroma.cn/R/segmentByPruneCBS.R
aroma.cn/R/RawAlleleBFractions.XTRAS.R
aroma.cn/R/callXXorXY.numeric.R
aroma.cn/R/CBS.findAtomicAberrations.R
aroma.cn/R/PairedPSCBS.NORM.R
aroma.cn/R/normalizeMirroredBAFsByRegions.R
aroma.cn/R/PolarSnpData.R
aroma.cn/R/PairedPSCBS.findAtomicAberrations.R
aroma.cn/R/testEquality.R
aroma.cn/R/TotalFracBSnpData.R
aroma.cn/R/PairedPSCBS.CALL2.R
aroma.cn/R/PairedPSCBSFileSet.R
aroma.cn/R/PrincipalCurveNormalization.R
aroma.cn/R/MultiSourceCopyNumberNormalization.XTRAS.R
aroma.cn/R/006.fixVarArgs.R
aroma.cn/R/cnr.R
aroma.cn/R/calculatePairedPSCNByGenotype.R
aroma.cn/R/pruneCNA.R
aroma.cn/R/PeaksAndValleys.EXTS.R
aroma.cn/R/testAllelicBalanceByBAFs.R
aroma.cn/R/999.NonDocumentedObjects.R
aroma.cn/R/999.package.R
aroma.cn/R/fitLoessKD.matrix.R
aroma.cn/R/PairedPSCBSFile.R
aroma.cn/R/zzz.R
aroma.cn/R/C1C2.R
aroma.cn/R/AbstractCurveNormalization.R
aroma.cn/MD5
aroma.cn/DESCRIPTION
aroma.cn/man
aroma.cn/man/extractTupleOfDataFiles.MultiSourceCopyNumberNormalization.Rd
aroma.cn/man/getInputDataSets.MultiSourceCopyNumberNormalization.Rd
aroma.cn/man/XYCurveNormalization.Rd
aroma.cn/man/PrincipalCurveNormalization.Rd
aroma.cn/man/AbstractCurveNormalization.Rd
aroma.cn/man/fitOne.MultiSourceCopyNumberNormalization.Rd
aroma.cn/man/aroma.cn-package.Rd
aroma.cn/man/getSubsetToFit.MultiSourceCopyNumberNormalization.Rd
aroma.cn/man/normalizePrincipalCurve.matrix.Rd
aroma.cn/man/cnr.Rd
aroma.cn/man/TotalCnBinnedSmoothing.Rd
aroma.cn/man/getSmoothedDataSets.MultiSourceCopyNumberNormalization.Rd
aroma.cn/man/TotalCnKernelSmoothing.Rd
aroma.cn/man/TumorBoostNormalization.Rd
aroma.cn/man/callPeaks.PeaksAndValleys.Rd
aroma.cn/man/getFitAromaUgpFile.MultiSourceCopyNumberNormalization.Rd
aroma.cn/man/callCopyNeutralRegions.PairedPSCBS.Rd
aroma.cn/man/process.MultiSourceCopyNumberNormalization.Rd
aroma.cn/man/normalizeMirroredBAFsByRegions.matrix.Rd
aroma.cn/man/callXXorXY.numeric.Rd
aroma.cn/man/MultiSourceCopyNumberNormalization.Rd
aroma.cn/man/normalizeBAFsByRegions.PairedPSCBS.Rd
aroma.cn/man/testAllelicBalanceByBAFs.Rd
aroma.cn/man/getAllNames.MultiSourceCopyNumberNormalization.Rd
aroma.cn/man/findAtomicAberrations.CopyNumberRegions.Rd
aroma.cn/man/PairedPscbsModel.Rd
aroma.cn/man/callAllelicBalanceByBAFs.PairedPSCBS.Rd
aroma.cn/man/Non-documented_objects.Rd
aroma.cn/man/TotalCnSmoothing.Rd