Man pages for aroma.core
Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
| AbstractCNData | The AbstractCNData class |
| AbstractPSCNData | The AbstractPSCNData class |
| allocate.AromaTabularBinaryFile | Creates an AromaTabularBinaryFile |
| AromaCellCpgFile | A binary file holding local CpG density for each cell... |
| AromaCellPositionFile | A binary file holding chromosome/position for each cell |
| AromaCellTabularBinaryFile | The AromaCellTabularBinaryFile class |
| aroma.core-package | Package aroma.core |
| AromaGenomeTextFile | The AromaGenomeTextFile class |
| AromaMicroarrayDataFile | The abstract AromaMicroarrayDataFile class |
| AromaMicroarrayDataSet | The AromaMicroarrayDataSet class |
| AromaMicroarrayDataSetTuple | The AromaMicroarrayDataSetTuple class |
| AromaMicroarrayTabularBinaryFile | The AromaMicroarrayTabularBinaryFile class |
| AromaPlatform | The AromaPlatform class |
| AromaPlatformInterface | The AromaPlatformInterface class |
| AromaRepository | The AromaRepository class |
| AromaTabularBinaryFile | The AromaTabularBinaryFile class |
| AromaTabularBinarySet | The AromaTabularBinarySet class |
| AromaTransform | The AromaTransform class |
| AromaUnitCallFile | The AromaUnitCallFile class |
| AromaUnitCallSet | The AromaUnitCallSet class |
| AromaUnitFracBCnBinaryFile | The AromaUnitFracBCnBinaryFile class |
| AromaUnitFracBCnBinarySet | The AromaUnitFracBCnBinarySet class |
| AromaUnitGenotypeCallFile | The AromaUnitGenotypeCallFile class |
| AromaUnitGenotypeCallSet | The AromaUnitGenotypeCallSet class |
| AromaUnitPscnBinaryFile | The AromaUnitPscnBinaryFile class |
| AromaUnitPscnBinarySet | The AromaUnitPscnBinarySet class |
| AromaUnitSignalBinaryFile | The AromaUnitSignalBinaryFile class |
| AromaUnitSignalBinarySet | The AromaUnitSignalBinarySet class |
| AromaUnitTabularBinaryFile | The AromaUnitTabularBinaryFile class |
| AromaUnitTotalCnBinaryFile | The AromaUnitTotalCnBinaryFile class |
| AromaUnitTotalCnBinarySet | The AromaUnitTotalCnBinarySet class |
| AromaUnitTypesFile | The AromaUnitTypesFile class |
| as.GrayscaleImage.matrix | Creates a Grayscale (Color) Image from a matrix file |
| BinnedScatter | The BinnedScatter class |
| CacheKeyInterface | The CacheKeyInterface class interface |
| CbsModel | The CbsModel class |
| ChromosomalModel | The ChromosomalModel class |
| ChromosomeExplorer | The ChromosomeExplorer class |
| colBinnedSmoothing.matrix | Binned smoothing of a matrix column by column |
| colKernelSmoothing.matrix | Kernel smoothing of a matrix column by column |
| CopyNumberChromosomalModel | The CopyNumberChromosomalModel class |
| CopyNumberSegmentationModel | The CopyNumberSegmentationModel class |
| display.Explorer | Displays the explorer in the default browser |
| doCBS | Performs Circular Binary Segmentation (CBS) on a data set |
| downloadChipTypeFile.AromaRepository | Download a particular chip type annotation file |
| downloadFile.AromaRepository | Download a particular file from the repository |
| estimateSds.CopyNumberChromosomalModel | Estimates the standard deviation of the raw copy numbers... |
| estimateStandardDeviation.RawGenomicSignals | Estimates the standard deviation of the raw Ys |
| Explorer | The Explorer class |
| exportAromaUnitPscnBinarySet | Export total and allele B signal data sets as a unified... |
| extractRawCopyNumbers.CopyNumberChromosomalModel | Extracts relative copy numbers |
| FileCacheKeyInterface | The FileCacheKeyInterface class interface |
| findAnnotationData | Locates an annotation data file |
| findAnnotationDataByChipType | Locates an annotation data file by its chip type |
| findFilesTodo.AromaTransform | Finds files in the data set still not processed |
| fit.CopyNumberChromosomalModel | Fits the model |
| fit.CopyNumberSegmentationModel | Fits the model |
| fitGenotypeConeBySfit.matrix | Fits an affine transformation to allele A and allele B data |
| fitGenotypeCone.matrix | Fits an affine transformation to allele A and allele B data |
| fitMultiDimensionalCone.matrix | Fits an affine transformation to multi-dimensional data |
| getAlias.Explorer | Gets the alias of the output set |
| getAromaPlatform.AromaPlatformInterface | Gets the platform |
| getCacheKey.CacheKeyInterface | Gets a list of cache key items |
| getCacheKey.FileCacheKeyInterface | Gets a list of cache key items |
| getChipType.AromaPlatformInterface | Gets the chip type |
| getChipType.ChromosomalModel | Gets a label for all chip types merged |
| getChromosomes.ChromosomalModel | Gets the chromosomes to be processed |
| getChromosomes.ChromosomeExplorer | Gets the chromosomes available |
| getFullName.AromaTransform | Gets the full name of the output data set |
| getInputDataSet.AromaTransform | Gets the input data set |
| getModel.ChromosomeExplorer | Gets the model |
| getName.AromaTransform | Gets the name of the output data set |
| getName.Explorer | Gets the name of the explorer |
| getNames.ChromosomalModel | Gets the names of the arrays |
| getNames.Explorer | Gets the names of the input samples |
| getOutputDataSet.AromaTransform | Gets the transformed data set |
| getParametersAsString.ParametersInterface | Gets the parameters as character |
| getParameters.ParametersInterface | Gets a list of parameters |
| getPath.AromaTransform | Gets the path of the output directory |
| getPath.Explorer | Gets the path of the output directory |
| getPlatform.AromaPlatformInterface | Gets the platform |
| getRootPath.AromaTransform | Gets the root path of the output directory |
| getRootPath.Explorer | Gets the root path of the output directory |
| getTags.AromaTransform | Gets the tags of the output data set |
| getTags.Explorer | Gets the tags of the explorer |
| getUnitAnnotationDataFile.AromaPlatformInterface | Gets a unit annotation data file of a particular class |
| GladModel | The GladModel class |
| HaarSegModel | The HaarSegModel class |
| indexOf.UnitNamesFile | Gets the indices of units by their names |
| isCompatibleWith.AromaPlatformInterface | Checks if a particular unit annotation data file is... |
| isDone.AromaTransform | Checks if the data set is processed or not |
| listFiles.AromaRepository | Retrieves the files available on the repository under a... |
| matrixBlockPolish.matrix | Applies a polishing function to blocks of rows and columns... |
| mergeBoxplotStats.list | Merges a list of boxplot.stats() elements |
| nbrOfArrays.ChromosomalModel | Gets the number of arrays |
| nbrOfArrays.Explorer | Gets the total number of arrays |
| nbrOfChipTypes.AromaMicroarrayDataSetTuple | Gets the number of chip types |
| nbrOfChipTypes.ChromosomalModel | Gets the number of chip types |
| Non-documented_objects | Non-documented objects |
| NonPairedPSCNData | The NonPairedPSCNData class |
| PairedPSCNData | The PairedPSCNData class |
| ParametersInterface | The ParametersInterface class interface |
| plotTracks.PairedPSCNData | Plots parental specific copy numbers along the genome |
| process.AromaTransform | Processes the data set |
| process.ChromosomeExplorer | Generates image files, scripts and dynamic pages for the... |
| process.Explorer | Generates image files, scripts and dynamic pages for the... |
| processTime | Gets the running time of the R process and its children... |
| RawAlleleBFractions | The RawAlleleBFractions class |
| RawCopyNumberModel | The RawCopyNumberModel class |
| RawCopyNumbers | The RawCopyNumbers class |
| RawGenomicSignals | The RawGenomicSignals class |
| RawMirroredAlleleBFractions | The RawMirroredAlleleBFractions class |
| RawSequenceReads | The RawSequenceReads class |
| readFooter.AromaTabularBinaryFile | Reads the file footer in XML format into a named nested list |
| segmentByCBS.RawGenomicSignals | Segment copy numbers using the CBS method |
| segmentByGLAD.RawGenomicSignals | Segment copy numbers using the GLAD method |
| segmentByHaarSeg.RawGenomicSignals | Segment copy numbers using the HaarSeg method |
| segmentByMPCBS.RawGenomicSignals | Segment copy numbers using the multi-platform CBS (mpCBS)... |
| SegmentedAlleleBFractions | The SegmentedAlleleBFractions class |
| SegmentedCopyNumbers | The SegmentedCopyNumbers class |
| SegmentedGenomicSignalsInterface | The SegmentedGenomicSignalsInterface class interface |
| setAlias.Explorer | Sets the alias of the output set |
| setArrays.ChromosomeExplorer | Sets the arrays |
| setArrays.Explorer | Sets the arrays |
| UnitAnnotationDataFile | The UnitAnnotationDataFile interface class |
| UnitNamesFile | The UnitNamesFile interface class |
| UnitTypesFile | The UnitTypesFile interface class |
| updateSetupExplorerFile.ChromosomeExplorer | Updates the Javascript file |
| writeDataFrame.AromaUnitSignalBinaryFile | Writes the data file as a tab-delimited text file |
| writeDataFrame.AromaUnitSignalBinarySet | Writes the data set as a tab-delimited text file |
| writeDataFrame.AromaUnitTabularBinaryFile | Writes the data file as a tab-delimited text file |
| writeFooter.AromaTabularBinaryFile | Writes a named nested list to the file footer in XML format |
