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aroma.core  

Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
View on CRAN: Click here


Download and install aroma.core package within the R console
Install from CRAN:
install.packages("aroma.core")

Install from Github:
library("remotes")
install_github("cran/aroma.core")

Install by package version:
library("remotes")
install_version("aroma.core", "3.3.1")



Attach the package and use:
library("aroma.core")
Maintained by
Henrik Bengtsson
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2009-06-16
Latest Update: 2024-02-19
Description:
Core methods and classes used by higher-level 'aroma.*' packages part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'.
How to cite:
Henrik Bengtsson (2009). aroma.core: Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework. R package version 3.3.1, https://cran.r-project.org/web/packages/aroma.core. Accessed 06 Nov. 2024.
Previous versions and publish date:
1.1.2 (2009-06-16 08:40), 1.2.0 (2009-09-10 13:34), 1.3.1 (2009-11-03 20:31), 1.4.0 (2010-01-07 16:41), 1.5.0 (2010-02-23 12:30), 1.6.0 (2010-05-16 18:15), 1.7.0 (2010-07-26 13:49), 1.8.0 (2010-11-08 08:31), 1.8.1 (2010-12-06 08:48), 1.9.0 (2011-01-10 15:37), 1.9.1 (2011-01-15 17:23), 2.0.0 (2011-02-17 14:07), 2.1.0 (2011-04-09 11:28), 2.1.3 (2011-08-01 07:16), 2.1.4 (2011-08-02 12:32), 2.1.5 (2011-08-31 06:11), 2.2.0 (2011-09-03 06:49), 2.2.2 (2011-10-19 09:39), 2.3.0 (2011-11-02 18:25), 2.3.2 (2011-11-15 07:49), 2.4.1 (2012-01-12 17:32), 2.5.0 (2012-03-26 08:06), 2.6.0 (2012-09-06 07:21), 2.7.0 (2012-11-25 09:16), 2.8.0 (2012-12-22 10:47), 2.9.0 (2013-04-25 07:17), 2.10.0 (2013-08-04 10:06), 2.11.0 (2013-10-17 07:59), 2.12.1 (2014-03-08 07:16), 2.13.0 (2015-01-17 00:16), 2.13.1 (2015-05-26 08:14), 2.14.0 (2015-10-21 10:01), 3.0.0 (2016-01-06 10:01), 3.1.0 (2017-03-23 14:10), 3.1.1 (2017-09-13 09:24), 3.1.2 (2018-04-24 10:08), 3.1.3 (2018-05-03 15:42), 3.2.0 (2019-06-17 20:20), 3.2.1 (2020-02-04 16:20), 3.2.2 (2021-01-05 06:10), 3.3.0 (2022-11-15 19:30)
Other packages that cited aroma.core R package
View aroma.core citation profile
Other R packages that aroma.core depends, imports, suggests or enhances
Complete documentation for aroma.core
Functions, R codes and Examples using the aroma.core R package
Some associated functions: AbstractCNData . AbstractPSCNData . AromaCellCpgFile . AromaCellPositionFile . AromaCellTabularBinaryFile . AromaGenomeTextFile . AromaMicroarrayDataFile . AromaMicroarrayDataSet . AromaMicroarrayDataSetTuple . AromaMicroarrayTabularBinaryFile . AromaPlatform . AromaPlatformInterface . AromaRepository . AromaTabularBinaryFile . AromaTabularBinarySet . AromaTransform . AromaUnitCallFile . AromaUnitCallSet . AromaUnitFracBCnBinaryFile . AromaUnitFracBCnBinarySet . AromaUnitGenotypeCallFile . AromaUnitGenotypeCallSet . AromaUnitPscnBinaryFile . AromaUnitPscnBinarySet . AromaUnitSignalBinaryFile . AromaUnitSignalBinarySet . AromaUnitTabularBinaryFile . AromaUnitTotalCnBinaryFile . AromaUnitTotalCnBinarySet . AromaUnitTypesFile . BinnedScatter . CacheKeyInterface . CbsModel . ChromosomalModel . ChromosomeExplorer . CopyNumberChromosomalModel . CopyNumberSegmentationModel . Explorer . FileCacheKeyInterface . GladModel . HaarSegModel . Non-documented_objects . NonPairedPSCNData . PairedPSCNData . ParametersInterface . RawAlleleBFractions . RawCopyNumberModel . RawCopyNumbers . RawGenomicSignals . RawMirroredAlleleBFractions . RawSequenceReads . SegmentedAlleleBFractions . SegmentedCopyNumbers . SegmentedGenomicSignalsInterface . UnitAnnotationDataFile . UnitNamesFile . UnitTypesFile . allocate.AromaTabularBinaryFile . aroma.core-package . as.GrayscaleImage.matrix . colBinnedSmoothing.matrix . colKernelSmoothing.matrix . display.Explorer . doCBS . downloadChipTypeFile.AromaRepository . downloadFile.AromaRepository . estimateSds.CopyNumberChromosomalModel . estimateStandardDeviation.RawGenomicSignals . exportAromaUnitPscnBinarySet . extractRawCopyNumbers.CopyNumberChromosomalModel . findAnnotationData . findAnnotationDataByChipType . findFilesTodo.AromaTransform . fit.CopyNumberChromosomalModel . fit.CopyNumberSegmentationModel . fitGenotypeCone.matrix . fitGenotypeConeBySfit.matrix . fitMultiDimensionalCone.matrix . getAlias.Explorer . getAromaPlatform.AromaPlatformInterface . getCacheKey.CacheKeyInterface . getCacheKey.FileCacheKeyInterface . getChipType.AromaPlatformInterface . getChipType.ChromosomalModel . getChromosomes.ChromosomalModel . getChromosomes.ChromosomeExplorer . getFullName.AromaTransform . getInputDataSet.AromaTransform . getModel.ChromosomeExplorer . getName.AromaTransform . getName.Explorer . getNames.ChromosomalModel . getNames.Explorer . getOutputDataSet.AromaTransform . getParameters.ParametersInterface . getParametersAsString.ParametersInterface . getPath.AromaTransform . getPath.Explorer . getPlatform.AromaPlatformInterface . getRootPath.AromaTransform . getRootPath.Explorer . getTags.AromaTransform . getTags.Explorer . getUnitAnnotationDataFile.AromaPlatformInterface . indexOf.UnitNamesFile . isCompatibleWith.AromaPlatformInterface . isDone.AromaTransform . listFiles.AromaRepository . matrixBlockPolish.matrix . mergeBoxplotStats.list . nbrOfArrays.ChromosomalModel . nbrOfArrays.Explorer . nbrOfChipTypes.AromaMicroarrayDataSetTuple . nbrOfChipTypes.ChromosomalModel . plotTracks.PairedPSCNData . process.AromaTransform . process.ChromosomeExplorer . process.Explorer . processTime . readFooter.AromaTabularBinaryFile . segmentByCBS.RawGenomicSignals . segmentByGLAD.RawGenomicSignals . segmentByHaarSeg.RawGenomicSignals . segmentByMPCBS.RawGenomicSignals . setAlias.Explorer . setArrays.ChromosomeExplorer . setArrays.Explorer . updateSetupExplorerFile.ChromosomeExplorer . writeDataFrame.AromaUnitSignalBinaryFile . writeDataFrame.AromaUnitSignalBinarySet . writeDataFrame.AromaUnitTabularBinaryFile . writeFooter.AromaTabularBinaryFile . 
Some associated R codes: 000.R . 006.fixVarArgs.R . 008.BioC.R . 009.setup.R . 998.AromaPackage.R . 999.AromaCore.R . 999.NonDocumentedObjects.R . 999.package.R . AbstractCNData.R . AbstractPSCNData.R . Arguments.EXTRAS.R . AromaCellCpgFile.R . AromaCellPositionFile.R . AromaCellSequenceFile.R . AromaCellSequenceFile.REPEATS.R . AromaCellSequenceFile.SNPs.R . AromaCellTabularBinaryFile.R . AromaGenomeTextFile.R . AromaMicroarrayDataFile.ATTRS.R . AromaMicroarrayDataFile.PLOT.R . AromaMicroarrayDataFile.R . AromaMicroarrayDataSet.ATTRS.R . AromaMicroarrayDataSet.EXT.R . AromaMicroarrayDataSet.R . AromaMicroarrayDataSetTuple.R . AromaMicroarrayTabularBinaryFile.R . AromaNnn.getRootName.R . AromaPlatform.R . AromaPlatformInterface.R . AromaRepository.R . AromaSettings.R . AromaTabularBinaryFile.R . AromaTabularBinarySet.ATTRS.R . AromaTabularBinarySet.R . AromaTransform.R . AromaUcscGenomeTextFile.R . AromaUflFile.R . AromaUgpFile.R . AromaUgpFile.plotCoverageMap.R . AromaUnitCallFile.R . AromaUnitCallSet.R . AromaUnitChromosomeTabularBinaryFile.R . AromaUnitFracBCnBinaryFile.R . AromaUnitFracBCnBinarySet.R . AromaUnitFracBCnBinarySet.exportFracBDiffSet.R . AromaUnitGcContentFile.R . AromaUnitGenotypeCallFile.R . AromaUnitGenotypeCallSet.R . AromaUnitPscnBinaryFile.R . AromaUnitPscnBinarySet.R . AromaUnitSignalBinaryFile.R . AromaUnitSignalBinaryFile.writeDataFrame.R . AromaUnitSignalBinarySet.R . AromaUnitSignalBinarySet.writeDataFrame.R . AromaUnitTabularBinaryFile.R . AromaUnitTabularBinaryFile.writeDataFrame.R . AromaUnitTotalCnBinaryFile.R . AromaUnitTotalCnBinaryFile.extractPSCNArray.R . AromaUnitTotalCnBinaryFile.xam.R . AromaUnitTotalCnBinaryFileList.R . AromaUnitTotalCnBinarySet.R . AromaUnitTotalCnBinarySet.exportAromaUnitPscnBinarySet.R . AromaUnitTotalCnBinarySet.exportTotalCnRatioSet.R . AromaUnitTotalCnBinarySetTuple.R . AromaUnitTypesFile.R . BasicObject.asThis.R . BinnedScatter.R . CacheKeyInterface.R . CbsModel.R . CbsSegmentationDataFile.R . CbsSegmentationDataSet.R . ChromosomalModel.R . ChromosomalModel.drawCytoband.R . ChromosomeExplorer.LAYERS.R . ChromosomeExplorer.R . CopyNumberChromosomalModel.R . CopyNumberChromosomalModel.newPlot.R . CopyNumberChromosomalModel.plotChromosomesLayers.R . CopyNumberChromosomalModel.plotFitLayers.R . CopyNumberChromosomalModel.plotRawCopyNumbers.R . CopyNumberChromosomalModel.plotSampleLayers.R . CopyNumberDataSetTuple.R . CopyNumberOutliers.FOREIGN.R . CopyNumberOutliers.R . CopyNumberRegions.EXT.R . CopyNumberRegions.EXT2.R . CopyNumberRegions.PLOT.R . CopyNumberRegions.R . CopyNumberSegmentationModel.R . CopyNumberSegmentationModel.plot.R . CopyNumberSegmentationModel.plotCopyNumberRegionLayers.R . DNAcopy.EXTS.R . Explorer.R . FileCacheKeyInterface.R . GLAD.EXTS.R . GenericDataFileSet.getParentName.R . GenericTabularFileSet.calculateAverageColumnAcrossFiles.R . GladModel.R . GladModel.onFitAddGenotypeCalls.R . HaarSeg.EXTS.R . HaarSegModel.R . Image.EXTS.R . MPCBS.EXTS.R . NonPairedPSCNData.R . PairedPSCNData.PLOT.R . PairedPSCNData.R . ParametersInterface.R . ProbePositionEffects.R . RasterImage.R . RawAlleleBFractions.R . RawCopyNumberModel.R . RawCopyNumbers.R . RawGenomicSignals.OPS.R . RawGenomicSignals.PLOT.R . RawGenomicSignals.R . RawGenomicSignals.SEG.R . RawGenomicSignals.append.R . RawGenomicSignals.segmentByCBS.R . RawGenomicSignals.segmentByGLAD.R . RawGenomicSignals.segmentByHaarSeg.R . RawGenomicSignals.segmentByMPCBS.R . RawMirroredAlleleBFractions.R . RawSequenceReads.EXTRAS.R . RawSequenceReads.R . RichDataFrame.R . SampleAnnotationFile.R . SampleAnnotationSet.R . SegmentationDataFile.R . SegmentationDataSet.R . SegmentedAlleleBFracions.R . SegmentedCopyNumbers.R . SegmentedGenomicSignalsInterface.COLS.R . SegmentedGenomicSignalsInterface.R . TextUnitNamesFile.R . UnitAnnotationDataFile.R . UnitNamesFile.R . UnitTypesFile.R . backtransformGenotypeCone.matrix.R . backtransformMultiDimensionalCone.matrix.R . colBinnedSmoothing.R . colGaussianSmoothing.R . colKernelSmoothing.R . convertTable.R . doCBS.R . drawCytoband2.R . findAnnotationData.R . findAnnotationDataByChipType.R . findPngDevice.R . fitGenotypeCone.matrix.R . fitMultiDimensionalCone.matrix.R . fitSplineBlockPolish.matrix.R . fitWHLAPLM.matrix.R . fitWHRCModel.matrix.R . fitWRMA.matrix.R . getAromaFullNameTranslatorSet.R . getCommonListElements.R . getDeviceResolution.R . getProbePositionEffectDesignMatrix.R . kernelWeights.R . lapplyInChunks.R . library.patch.R . locallyUnique.R . matrixBlockPolish.matrix.R . mergeBoxplotStats.list.R . norm2d.matrix.R . normalizeGenotypeCone.R . private.Machine.R . processTime.R . profileCGH.drawExtraAnnotations.R . profileCGH.plotProfile2.R . profileCGH.plotRawCNs.R . remap.R . requireWithMemory.R . shakyText.R . simpleXml.R . smoothWRMA.matrix.R . smoothWSA.matrix.R . stextChipType.R . stringTree.R . transforms.R . utils.R . yellow.colors.R . zzz.R .  Full aroma.core package functions and examples
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