Files in HenrikBengtsson/aroma.core

Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

.Rbuildignore

.github/workflows/R-CMD-check.yaml

.github/workflows/covr.yaml

.gitignore

.make/Makefile

CONDUCT.md CONTRIBUTING.md

DESCRIPTION

Makefile

NAMESPACE

NEWS.md R/000.R R/006.fixVarArgs.R R/008.BioC.R R/009.setup.R R/998.AromaPackage.R R/999.AromaCore.R R/999.NonDocumentedObjects.R R/999.package.R R/AbstractCNData.R R/AbstractPSCNData.R R/Arguments.EXTRAS.R R/AromaCellCpgFile.R R/AromaCellPositionFile.R R/AromaCellSequenceFile.R R/AromaCellSequenceFile.REPEATS.R R/AromaCellSequenceFile.SNPs.R R/AromaCellTabularBinaryFile.R R/AromaGenomeTextFile.R R/AromaMicroarrayDataFile.ATTRS.R R/AromaMicroarrayDataFile.PLOT.R R/AromaMicroarrayDataFile.R R/AromaMicroarrayDataSet.ATTRS.R R/AromaMicroarrayDataSet.EXT.R R/AromaMicroarrayDataSet.R R/AromaMicroarrayDataSetTuple.R R/AromaMicroarrayTabularBinaryFile.R R/AromaNnn.getRootName.R R/AromaPlatform.R R/AromaPlatformInterface.R R/AromaRepository.R R/AromaSettings.R R/AromaTabularBinaryFile.R R/AromaTabularBinarySet.ATTRS.R R/AromaTabularBinarySet.R R/AromaTransform.R R/AromaUcscGenomeTextFile.R R/AromaUflFile.R R/AromaUgpFile.R R/AromaUgpFile.plotCoverageMap.R R/AromaUnitCallFile.R R/AromaUnitCallSet.R R/AromaUnitChromosomeTabularBinaryFile.R R/AromaUnitFracBCnBinaryFile.R R/AromaUnitFracBCnBinarySet.R R/AromaUnitFracBCnBinarySet.exportFracBDiffSet.R R/AromaUnitGcContentFile.R R/AromaUnitGenotypeCallFile.R R/AromaUnitGenotypeCallSet.R R/AromaUnitPscnBinaryFile.R R/AromaUnitPscnBinarySet.R R/AromaUnitSignalBinaryFile.R R/AromaUnitSignalBinaryFile.writeDataFrame.R R/AromaUnitSignalBinarySet.R R/AromaUnitSignalBinarySet.writeDataFrame.R R/AromaUnitTabularBinaryFile.R R/AromaUnitTabularBinaryFile.writeDataFrame.R R/AromaUnitTotalCnBinaryFile.R R/AromaUnitTotalCnBinaryFile.extractPSCNArray.R R/AromaUnitTotalCnBinaryFile.xam.R R/AromaUnitTotalCnBinaryFileList.R R/AromaUnitTotalCnBinarySet.R R/AromaUnitTotalCnBinarySet.exportAromaUnitPscnBinarySet.R R/AromaUnitTotalCnBinarySet.exportTotalCnRatioSet.R R/AromaUnitTotalCnBinarySetTuple.R R/AromaUnitTypesFile.R R/BasicObject.asThis.R R/BinnedScatter.R R/CacheKeyInterface.R R/CbsModel.R R/CbsSegmentationDataFile.R R/CbsSegmentationDataSet.R R/ChromosomalModel.R R/ChromosomalModel.drawCytoband.R R/ChromosomeExplorer.LAYERS.R R/ChromosomeExplorer.R R/CopyNumberChromosomalModel.R R/CopyNumberChromosomalModel.newPlot.R R/CopyNumberChromosomalModel.plotChromosomesLayers.R R/CopyNumberChromosomalModel.plotFitLayers.R R/CopyNumberChromosomalModel.plotRawCopyNumbers.R R/CopyNumberChromosomalModel.plotSampleLayers.R R/CopyNumberDataSetTuple.R R/CopyNumberOutliers.FOREIGN.R R/CopyNumberOutliers.R R/CopyNumberRegions.EXT.R R/CopyNumberRegions.EXT2.R R/CopyNumberRegions.PLOT.R R/CopyNumberRegions.R R/CopyNumberSegmentationModel.R R/CopyNumberSegmentationModel.plot.R R/CopyNumberSegmentationModel.plotCopyNumberRegionLayers.R R/DNAcopy.EXTS.R R/Explorer.R R/FileCacheKeyInterface.R R/GLAD.EXTS.R R/GenericDataFileSet.getParentName.R R/GenericTabularFileSet.calculateAverageColumnAcrossFiles.R R/GladModel.R R/GladModel.onFitAddGenotypeCalls.R R/HaarSeg.EXTS.R R/HaarSegModel.R R/Image.EXTS.R R/MPCBS.EXTS.R R/NonPairedPSCNData.R R/PairedPSCNData.PLOT.R R/PairedPSCNData.R R/ParametersInterface.R R/ProbePositionEffects.R R/RasterImage.R R/RawAlleleBFractions.R R/RawCopyNumberModel.R R/RawCopyNumbers.R R/RawGenomicSignals.OPS.R R/RawGenomicSignals.PLOT.R R/RawGenomicSignals.R R/RawGenomicSignals.SEG.R R/RawGenomicSignals.append.R R/RawGenomicSignals.segmentByCBS.R R/RawGenomicSignals.segmentByGLAD.R R/RawGenomicSignals.segmentByHaarSeg.R R/RawGenomicSignals.segmentByMPCBS.R R/RawMirroredAlleleBFractions.R R/RawSequenceReads.EXTRAS.R R/RawSequenceReads.R R/RichDataFrame.R R/SampleAnnotationFile.R R/SampleAnnotationSet.R R/SegmentationDataFile.R R/SegmentationDataSet.R R/SegmentedAlleleBFracions.R R/SegmentedCopyNumbers.R R/SegmentedGenomicSignalsInterface.COLS.R R/SegmentedGenomicSignalsInterface.R R/TextUnitNamesFile.R R/UnitAnnotationDataFile.R R/UnitNamesFile.R R/UnitTypesFile.R R/backtransformGenotypeCone.matrix.R R/backtransformMultiDimensionalCone.matrix.R R/colBinnedSmoothing.R R/colGaussianSmoothing.R R/colKernelSmoothing.R R/convertTable.R R/doCBS.R R/drawCytoband2.R R/findAnnotationData.R R/findAnnotationDataByChipType.R R/findPngDevice.R R/fitGenotypeCone.matrix.R R/fitMultiDimensionalCone.matrix.R R/fitSplineBlockPolish.matrix.R R/fitWHLAPLM.matrix.R R/fitWHRCModel.matrix.R R/fitWRMA.matrix.R R/getAromaFullNameTranslatorSet.R R/getCommonListElements.R R/getDeviceResolution.R R/getProbePositionEffectDesignMatrix.R R/kernelWeights.R R/lapplyInChunks.R R/library.patch.R R/locallyUnique.R R/matrixBlockPolish.matrix.R R/mergeBoxplotStats.list.R R/norm2d.matrix.R R/normalizeGenotypeCone.R R/private.Machine.R R/processTime.R R/profileCGH.drawExtraAnnotations.R R/profileCGH.plotProfile2.R R/profileCGH.plotRawCNs.R R/remap.R R/requireWithMemory.R R/shakyText.R R/simpleXml.R R/smoothWRMA.matrix.R R/smoothWSA.matrix.R R/stextChipType.R R/stringTree.R R/transforms.R R/utils.R R/yellow.colors.R R/zzz.R README.md cran-comments.md

incl/999.missingdocs.txt

incl/AromaGenomeTextFile.Rex

incl/AromaPlatform.Rex

incl/BengtssonH_2003.bib.Rdoc

incl/BinnedScatter.Rex

incl/RawCopyNumbers.Rex

incl/RawGenomicSignals.OPS.Rex

incl/RawGenomicSignals.SEG,MP.Rex

incl/RawGenomicSignals.SEG.Rex

incl/SegmentedCopyNumbers.Rex

incl/colBinnedSmoothing.Rex

incl/colKernelSmoothing.Rex

incl/doCBS.Rex

incl/fitGenotypeCone.matrix.Rex

incl/fitGenotypeConeBySfit.matrix.Rex

incl/fitMultiDimensionalCone.matrix.Rex

incl/matrixBlockPolish.matrix.Rex

incl/mergeBoxplotStats.list.Rex

inst/WORDLIST

inst/annotationData/genomes/Canine/Canine,chromosomes,UGP,HB20100822.txt

inst/annotationData/genomes/Human/Human,chromosomes.txt

inst/annotationData/genomes/Human/Human,cytobands,hg17,GLADv2.4.0,HB20100219.txt

inst/annotationData/genomes/Mouse/Mouse,chromosomes.txt

inst/bin/nohupR

inst/reports/includes/css/ArrayExplorer.css

inst/reports/includes/css/ChromosomeExplorer.css

inst/reports/includes/css/R.css

inst/reports/includes/css/figures.css

inst/reports/includes/css/rsp.css

inst/reports/includes/images/indicator.gif

inst/reports/includes/images/indicator_medium.gif

inst/reports/includes/images/pixelWhite.png

inst/reports/includes/js/ArrayExplorer/ArrayExplorer.js

inst/reports/includes/js/ArrayExplorer/HISTORY

inst/reports/includes/js/ChromosomeExplorer/ChromosomeExplorer.js

inst/reports/includes/js/ChromosomeExplorer/HISTORY

inst/reports/includes/js/ScrollImage2d.js

inst/reports/includes/js/Scrollbar2d.js

inst/reports/includes/js/Webcuts.js

inst/reports/includes/js/domUtils.js

inst/reports/includes/js/require.js

inst/reports/templates/html/ArrayExplorer/ArrayExplorer.html

inst/reports/templates/html/ArrayExplorer/about.html

inst/reports/templates/html/ArrayExplorer/help.html

inst/reports/templates/html/ChromosomeExplorer/ChromosomeExplorer.html

inst/reports/templates/html/ChromosomeExplorer/help.html

inst/reports/templates/html/ChromosomeExplorer/index.html

inst/reports/templates/rsp/ArrayExplorer/setupExplorer.js.rsp

inst/reports/templates/rsp/ChromosomeExplorer/setupExplorer.js.rsp

inst/testScripts/fileFormats/acf/test20090105,acf.R inst/testScripts/fileFormats/acf/test20090107,AromaUnitGenotypeCallSet.R inst/testScripts/fileFormats/acf/test20090518,acf.R inst/testScripts/fileFormats/acs/test20080804,acs.R

inst/testScripts/system/CnSegmentation/test20090510,SEG,weighted.Rex

inst/testScripts/system/CnSegmentation/test20090510,SEG.Rex

inst/testScripts/system/CnSegmentation/test20100222,SEG,symmetry.Rex

inst/testScripts/system/RawAlleleBFractions/test20090510,FracB.Rex

inst/testScripts/system/RawGenomicSignals/test20090510,Ops.Rex

inst/testScripts/system/RawGenomicSignals/test20090628,binSmoothing.Rex

inst/testScripts/system/RawGenomicSignals/test20090628,binSmoothingByState.Rex

inst/testScripts/system/UGP/test20090508,UGP.Rex

man/AbstractCNData.Rd man/AbstractPSCNData.Rd man/AromaCellCpgFile.Rd man/AromaCellPositionFile.Rd man/AromaCellTabularBinaryFile.Rd man/AromaGenomeTextFile.Rd man/AromaMicroarrayDataFile.Rd man/AromaMicroarrayDataSet.Rd man/AromaMicroarrayDataSetTuple.Rd man/AromaMicroarrayTabularBinaryFile.Rd man/AromaPlatform.Rd man/AromaPlatformInterface.Rd man/AromaRepository.Rd man/AromaTabularBinaryFile.Rd man/AromaTabularBinarySet.Rd man/AromaTransform.Rd man/AromaUnitCallFile.Rd man/AromaUnitCallSet.Rd man/AromaUnitFracBCnBinaryFile.Rd man/AromaUnitFracBCnBinarySet.Rd man/AromaUnitGenotypeCallFile.Rd man/AromaUnitGenotypeCallSet.Rd man/AromaUnitPscnBinaryFile.Rd man/AromaUnitPscnBinarySet.Rd man/AromaUnitSignalBinaryFile.Rd man/AromaUnitSignalBinarySet.Rd man/AromaUnitTabularBinaryFile.Rd man/AromaUnitTotalCnBinaryFile.Rd man/AromaUnitTotalCnBinarySet.Rd man/AromaUnitTypesFile.Rd man/BinnedScatter.Rd man/CacheKeyInterface.Rd man/CbsModel.Rd man/ChromosomalModel.Rd man/ChromosomeExplorer.Rd man/CopyNumberChromosomalModel.Rd man/CopyNumberSegmentationModel.Rd man/Explorer.Rd man/FileCacheKeyInterface.Rd man/GladModel.Rd man/HaarSegModel.Rd man/Non-documented_objects.Rd man/NonPairedPSCNData.Rd man/PairedPSCNData.Rd man/ParametersInterface.Rd man/RawAlleleBFractions.Rd man/RawCopyNumberModel.Rd man/RawCopyNumbers.Rd man/RawGenomicSignals.Rd man/RawMirroredAlleleBFractions.Rd man/RawSequenceReads.Rd man/SegmentedAlleleBFractions.Rd man/SegmentedCopyNumbers.Rd man/SegmentedGenomicSignalsInterface.Rd man/UnitAnnotationDataFile.Rd man/UnitNamesFile.Rd man/UnitTypesFile.Rd man/allocate.AromaTabularBinaryFile.Rd man/aroma.core-package.Rd man/as.GrayscaleImage.matrix.Rd man/colBinnedSmoothing.matrix.Rd man/colKernelSmoothing.matrix.Rd man/display.Explorer.Rd man/doCBS.Rd man/downloadChipTypeFile.AromaRepository.Rd man/downloadFile.AromaRepository.Rd man/estimateSds.CopyNumberChromosomalModel.Rd man/estimateStandardDeviation.RawGenomicSignals.Rd man/exportAromaUnitPscnBinarySet.Rd man/extractRawCopyNumbers.CopyNumberChromosomalModel.Rd man/findAnnotationData.Rd man/findAnnotationDataByChipType.Rd man/findFilesTodo.AromaTransform.Rd man/fit.CopyNumberChromosomalModel.Rd man/fit.CopyNumberSegmentationModel.Rd man/fitGenotypeCone.matrix.Rd man/fitGenotypeConeBySfit.matrix.Rd man/fitMultiDimensionalCone.matrix.Rd man/getAlias.Explorer.Rd man/getAromaPlatform.AromaPlatformInterface.Rd man/getCacheKey.CacheKeyInterface.Rd man/getCacheKey.FileCacheKeyInterface.Rd man/getChipType.AromaPlatformInterface.Rd man/getChipType.ChromosomalModel.Rd man/getChromosomes.ChromosomalModel.Rd man/getChromosomes.ChromosomeExplorer.Rd man/getFullName.AromaTransform.Rd man/getInputDataSet.AromaTransform.Rd man/getModel.ChromosomeExplorer.Rd man/getName.AromaTransform.Rd man/getName.Explorer.Rd man/getNames.ChromosomalModel.Rd man/getNames.Explorer.Rd man/getOutputDataSet.AromaTransform.Rd man/getParameters.ParametersInterface.Rd man/getParametersAsString.ParametersInterface.Rd man/getPath.AromaTransform.Rd man/getPath.Explorer.Rd man/getPlatform.AromaPlatformInterface.Rd man/getRootPath.AromaTransform.Rd man/getRootPath.Explorer.Rd man/getTags.AromaTransform.Rd man/getTags.Explorer.Rd man/getUnitAnnotationDataFile.AromaPlatformInterface.Rd man/indexOf.UnitNamesFile.Rd man/isCompatibleWith.AromaPlatformInterface.Rd man/isDone.AromaTransform.Rd man/listFiles.AromaRepository.Rd man/matrixBlockPolish.matrix.Rd man/mergeBoxplotStats.list.Rd man/nbrOfArrays.ChromosomalModel.Rd man/nbrOfArrays.Explorer.Rd man/nbrOfChipTypes.AromaMicroarrayDataSetTuple.Rd man/nbrOfChipTypes.ChromosomalModel.Rd man/plotTracks.PairedPSCNData.Rd man/process.AromaTransform.Rd man/process.ChromosomeExplorer.Rd man/process.Explorer.Rd man/processTime.Rd man/readFooter.AromaTabularBinaryFile.Rd man/segmentByCBS.RawGenomicSignals.Rd man/segmentByGLAD.RawGenomicSignals.Rd man/segmentByHaarSeg.RawGenomicSignals.Rd man/segmentByMPCBS.RawGenomicSignals.Rd man/setAlias.Explorer.Rd man/setArrays.ChromosomeExplorer.Rd man/setArrays.Explorer.Rd man/updateSetupExplorerFile.ChromosomeExplorer.Rd man/writeDataFrame.AromaUnitSignalBinaryFile.Rd man/writeDataFrame.AromaUnitSignalBinarySet.Rd man/writeDataFrame.AromaUnitTabularBinaryFile.Rd man/writeFooter.AromaTabularBinaryFile.Rd revdep/README.md revdep/cran.md revdep/failures.md revdep/problems.md revdep/run.R

revdep/run.pbs

revdep/run.sge

tests/PairedPSCNData,SEG.R tests/PairedPSCNData.R tests/RawCopyNumbers,states.R tests/RawCopyNumbers.R tests/RawGenomicSignals.R tests/RawGenomicSignals.SEG,MP.R tests/RawGenomicSignals.SEG.R tests/RichDataFrame.R tests/SegmentedCopyNumbers.R tests/aromaSettings.R tests/binScatter.R tests/colBinnedSmoothing.R tests/colKernelSmoothing.R tests/fitGenotypeCone.R tests/fitMultiDimensionalCone.R tests/matrixBlockPolish.R tests/mergeBoxplotStats.R

HenrikBengtsson/aroma.core documentation built on Feb. 20, 2024, 9:17 p.m.