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

inst
inst/CITATION
inst/testScripts
inst/testScripts/setup
inst/testScripts/setup/01c.installAllPackages.R
inst/testScripts/setup/spawnTests.sh
inst/testScripts/setup/99a.cleanupRootDirectories.R inst/testScripts/setup/01a.downloadAllAnnotationData.R inst/testScripts/setup/01b.downloadAllRawDataSet.R
inst/testScripts/devel
inst/testScripts/devel/C1C2
inst/testScripts/devel/C1C2/21.PairedPSCBS,deShear,report.R inst/testScripts/devel/C1C2/31.PairedPSCBS,DP,deShear.R
inst/testScripts/system
inst/testScripts/system/CopyNumberProfiles
inst/testScripts/system/CopyNumberProfiles/20100909a,findAtomicAberrations.Rex
inst/testScripts/system/CopyNumberProfiles/20100911a,TumorClonality.Rex
inst/testScripts/system/CopyNumberProfiles/20100911b,TumorClonality,lineage.Rex
inst/testScripts/system/CopyNumberProfiles/20100909b,NormalContamination.Rex
inst/testScripts/system/CopyNumberProfiles/20100912b,Saturation.Rex
inst/testScripts/system/CopyNumberProfiles/20100912a,SegmentationStdError.Rex
inst/testScripts/system/segmentation
inst/testScripts/system/segmentation/20091110,CBS.Rex
inst/testScripts/system/MSLHN
inst/testScripts/system/MSLHN/20091218,TCGA,MSLHCN.Rex
inst/testScripts/system/pairedPSCN
inst/testScripts/system/pairedPSCN/R
inst/testScripts/system/pairedPSCN/R/loadAllDataSets.R inst/testScripts/system/pairedPSCN/R/00.setup.R inst/testScripts/system/pairedPSCN/R/getTumorNormalPairs.R inst/testScripts/system/pairedPSCN/R/zzz.R
inst/testScripts/system/pairedPSCN/genomicPlots.tex.rsp
inst/testScripts/system/CurveNormalization,OV
inst/testScripts/system/CurveNormalization,OV/test20090715a,waves.Rex
inst/testScripts/system/tracks
inst/testScripts/system/tracks/20091008,HCC1143,CRMAv2-dChip-GTC,plot.Rex
inst/testScripts/system/tracks/utils.R
inst/testScripts/system/tracks/20091010,TCGA,plot.Rex
inst/testScripts/system/TumorBoost
inst/testScripts/system/TumorBoost/test20090429b,TBN.Rex
inst/testScripts/system/TumorBoost/test20090429c,TBN,plot.Rex
inst/testScripts/system/TumorBoost/test20090429d,TBN,LOH,plot.Rex
inst/testScripts/system/TumorBoost/test20090429a,NGC.Rex
inst/testScripts/system/TumorBoost/test20090620a,NGC.Rex
inst/testScripts/system/MultiPlatform
inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,shifts.Rex
inst/testScripts/system/MultiPlatform/test20090209,TCGA,plot.Rex
inst/testScripts/system/MultiPlatform/test20090210,TCGA,MSCN,plot.Rex
inst/testScripts/system/MultiPlatform/test20090208,TCGA,MSCN.Rex
inst/testScripts/system/MultiPlatform/test20100102,TCGA,MSCN,mpCBS.Rex
inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,weights.Rex
inst/testScripts/system/MultiPlatform/test20090512,TCGA,MSCN,wCBS.Rex
inst/testScripts/system/MultiPlatform/test20090720,TCGA,MSCN,tracks.Rex
inst/testScripts/system/CondSegmentation
inst/testScripts/system/CondSegmentation/test20090927,TBN,plot.Rex
inst/testScripts/system/CondSegmentation/test20091014,TBN,plot.Rex
inst/testScripts/system/chipTypes
inst/testScripts/system/chipTypes/GenomeWideSNP_6
inst/testScripts/system/chipTypes/GenomeWideSNP_6/normalizeLoess2D.PairedPSCBS.Rex
inst/testScripts/system/chipTypes/GenomeWideSNP_6/calibrateC1C2.PairedPSCBS.Rex
inst/testScripts/system/chipTypes/GenomeWideSNP_6/calibrateC1C2,20111026.Rex
inst/testScripts/system/chipTypes/GenomeWideSNP_6/deShearC1C2.PairedPSCBS.Rex
inst/testScripts/system/chipTypes/GenomeWideSNP_6/orthogonalizeC1C2.PairedPSCBS.Rex
inst/templates
inst/templates/rsp
inst/templates/rsp/PairedPSCBS,deShear,report.tex.rsp
inst/templates/rsp/natbib.bst
inst/templates/rsp/bioinformatics-journals-abbr.bib
tests
tests/callAllelicBalanceByBAFs.PairedPSCBS.R tests/cnr.R
NAMESPACE
NEWS
R
R/principal.curve.pairs2.R R/NaiveFracBGenotyping.R R/CopyNumberRegions.findAtomicAberrations.R R/021.dynamic_imports.R R/TotalCnSmoothing.R R/XYCurveNormalization.R R/000.R R/normalizePrincipalCurve.matrix.R R/SnpData.R R/PrincipalCurve.XTRAS.R R/PairedPSCBS.PLOT3.R R/CartesianSnpData.R R/TotalCnKernelSmoothing.R R/PairedPSCBS.backgroundCorrect.R R/TumorBoostNormalization.R R/PairedPscbsModel.R R/AromaUnitPscnBinarySet.doSegmentByPairedPSCBS.R R/999.DEPRECATED.R R/RawGenotypeCalls.R R/PairedPSCBS.BOOT.R R/009.setup.R R/PairedPSCBS.fitC1C2Peaks.R R/PruneCNA.PLOT.R R/MultiSourceCopyNumberNormalization.R R/PruneCNA.EXTS.R R/TotalCnBinnedSmoothing.R R/PairedPscbsCaller.R R/segmentByPruneCBS.R R/RawAlleleBFractions.XTRAS.R R/callXXorXY.numeric.R R/CBS.findAtomicAberrations.R R/PairedPSCBS.NORM.R R/normalizeMirroredBAFsByRegions.R R/PolarSnpData.R R/PairedPSCBS.findAtomicAberrations.R R/testEquality.R R/TotalFracBSnpData.R R/PairedPSCBS.CALL2.R R/PairedPSCBSFileSet.R R/PrincipalCurveNormalization.R R/MultiSourceCopyNumberNormalization.XTRAS.R R/006.fixVarArgs.R R/cnr.R R/calculatePairedPSCNByGenotype.R R/pruneCNA.R R/PeaksAndValleys.EXTS.R R/testAllelicBalanceByBAFs.R R/999.NonDocumentedObjects.R R/999.package.R R/fitLoessKD.matrix.R R/PairedPSCBSFile.R R/zzz.R R/C1C2.R R/AbstractCurveNormalization.R
MD5
DESCRIPTION
man
man/extractTupleOfDataFiles.MultiSourceCopyNumberNormalization.Rd man/getInputDataSets.MultiSourceCopyNumberNormalization.Rd man/XYCurveNormalization.Rd man/PrincipalCurveNormalization.Rd man/AbstractCurveNormalization.Rd man/fitOne.MultiSourceCopyNumberNormalization.Rd man/aroma.cn-package.Rd man/getSubsetToFit.MultiSourceCopyNumberNormalization.Rd man/normalizePrincipalCurve.matrix.Rd man/cnr.Rd man/TotalCnBinnedSmoothing.Rd man/getSmoothedDataSets.MultiSourceCopyNumberNormalization.Rd man/TotalCnKernelSmoothing.Rd man/TumorBoostNormalization.Rd man/callPeaks.PeaksAndValleys.Rd man/getFitAromaUgpFile.MultiSourceCopyNumberNormalization.Rd man/callCopyNeutralRegions.PairedPSCBS.Rd man/process.MultiSourceCopyNumberNormalization.Rd man/normalizeMirroredBAFsByRegions.matrix.Rd man/callXXorXY.numeric.Rd man/MultiSourceCopyNumberNormalization.Rd man/normalizeBAFsByRegions.PairedPSCBS.Rd man/testAllelicBalanceByBAFs.Rd man/getAllNames.MultiSourceCopyNumberNormalization.Rd man/findAtomicAberrations.CopyNumberRegions.Rd man/PairedPscbsModel.Rd man/callAllelicBalanceByBAFs.PairedPSCBS.Rd man/Non-documented_objects.Rd man/TotalCnSmoothing.Rd
aroma.cn documentation built on May 29, 2017, 7:56 p.m.