Man pages for HenrikBengtsson/aroma.core
Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

AbstractCNDataThe AbstractCNData class
AbstractPSCNDataThe AbstractPSCNData class
allocate.AromaTabularBinaryFileCreates an AromaTabularBinaryFile
AromaCellCpgFileA binary file holding local CpG density for each cell...
AromaCellPositionFileA binary file holding chromosome/position for each cell
AromaCellTabularBinaryFileThe AromaCellTabularBinaryFile class
aroma.core-packagePackage aroma.core
AromaGenomeTextFileThe AromaGenomeTextFile class
AromaMicroarrayDataFileThe abstract AromaMicroarrayDataFile class
AromaMicroarrayDataSetThe AromaMicroarrayDataSet class
AromaMicroarrayDataSetTupleThe AromaMicroarrayDataSetTuple class
AromaMicroarrayTabularBinaryFileThe AromaMicroarrayTabularBinaryFile class
AromaPlatformThe AromaPlatform class
AromaPlatformInterfaceThe AromaPlatformInterface class
AromaRepositoryThe AromaRepository class
AromaTabularBinaryFileThe AromaTabularBinaryFile class
AromaTabularBinarySetThe AromaTabularBinarySet class
AromaTransformThe AromaTransform class
AromaUnitCallFileThe AromaUnitCallFile class
AromaUnitCallSetThe AromaUnitCallSet class
AromaUnitFracBCnBinaryFileThe AromaUnitFracBCnBinaryFile class
AromaUnitFracBCnBinarySetThe AromaUnitFracBCnBinarySet class
AromaUnitGenotypeCallFileThe AromaUnitGenotypeCallFile class
AromaUnitGenotypeCallSetThe AromaUnitGenotypeCallSet class
AromaUnitPscnBinaryFileThe AromaUnitPscnBinaryFile class
AromaUnitPscnBinarySetThe AromaUnitPscnBinarySet class
AromaUnitSignalBinaryFileThe AromaUnitSignalBinaryFile class
AromaUnitSignalBinarySetThe AromaUnitSignalBinarySet class
AromaUnitTabularBinaryFileThe AromaUnitTabularBinaryFile class
AromaUnitTotalCnBinaryFileThe AromaUnitTotalCnBinaryFile class
AromaUnitTotalCnBinarySetThe AromaUnitTotalCnBinarySet class
AromaUnitTypesFileThe AromaUnitTypesFile class
as.GrayscaleImage.matrixCreates a Grayscale (Color) Image from a matrix file
BinnedScatterThe BinnedScatter class
CacheKeyInterfaceThe CacheKeyInterface class interface
CbsModelThe CbsModel class
ChromosomalModelThe ChromosomalModel class
ChromosomeExplorerThe ChromosomeExplorer class
colBinnedSmoothing.matrixBinned smoothing of a matrix column by column
colKernelSmoothing.matrixKernel smoothing of a matrix column by column
CopyNumberChromosomalModelThe CopyNumberChromosomalModel class
CopyNumberSegmentationModelThe CopyNumberSegmentationModel class
display.ExplorerDisplays the explorer in the default browser
doCBSPerforms Circular Binary Segmentation (CBS) on a data set
downloadChipTypeFile.AromaRepositoryDownload a particular chip type annotation file
downloadFile.AromaRepositoryDownload a particular file from the reposity
estimateSds.CopyNumberChromosomalModelEstimates the standard deviation of the raw copy numbers...
estimateStandardDeviation.RawGenomicSignalsEstimates the standard deviation of the raw Ys
ExplorerThe Explorer class
exportAromaUnitPscnBinarySetExport total and allele B signal data sets as a unified...
extractRawCopyNumbers.CopyNumberChromosomalModelExtracts relative copy numbers
FileCacheKeyInterfaceThe FileCacheKeyInterface class interface
findAnnotationDataLocates an annotation data file
findAnnotationDataByChipTypeLocates an annotation data file by its chip type
findFilesTodo.AromaTransformFinds files in the data set still not processed
fit.CopyNumberChromosomalModelFits the model
fit.CopyNumberSegmentationModelFits the model
fitGenotypeConeBySfit.matrixFits an affine transformation to allele A and allele B data
fitGenotypeCone.matrixFits an affine transformation to allele A and allele B data
fitMultiDimensionalCone.matrixFits an affine transformation to multi-dimensional data
getAlias.ExplorerGets the alias of the output set
getAromaPlatform.AromaPlatformInterfaceGets the platform
getCacheKey.CacheKeyInterfaceGets a list of cache key items
getCacheKey.FileCacheKeyInterfaceGets a list of cache key items
getChipType.AromaPlatformInterfaceGets the chip type
getChipType.ChromosomalModelGets a label for all chip types merged
getChromosomes.ChromosomalModelGets the chromosomes to be processed
getChromosomes.ChromosomeExplorerGets the chromosomes available
getFullName.AromaTransformGets the full name of the output data set
getInputDataSet.AromaTransformGets the input data set
getModel.ChromosomeExplorerGets the model
getName.AromaTransformGets the name of the output data set
getName.ExplorerGets the name of the explorer
getNames.ChromosomalModelGets the names of the arrays
getNames.ExplorerGets the names of the input samples
getOutputDataSet.AromaTransformGets the transformed data set
getParametersAsString.ParametersInterfaceGets the parameters as character
getParameters.ParametersInterfaceGets a list of parameters
getPath.AromaTransformGets the path of the output directory
getPath.ExplorerGets the path of the output directory
getPlatform.AromaPlatformInterfaceGets the platform
getRootPath.AromaTransformGets the root path of the output directory
getRootPath.ExplorerGets the root path of the output directory
getTags.AromaTransformGets the tags of the output data set
getTags.ExplorerGets the tags of the explorer
getUnitAnnotationDataFile.AromaPlatformInterfaceGets a unit annotation data file of a particular class
GladModelThe GladModel class
HaarSegModelThe HaarSegModel class
indexOf.UnitNamesFileGets the indices of units by their names
isCompatibleWith.AromaPlatformInterfaceChecks if a particular unit annotation data file is...
isDone.AromaTransformChecks if the data set is processed or not
listFiles.AromaRepositoryRetrieves the files available on the repository under a...
matrixBlockPolish.matrixApplies a polishing function to blocks of rows and columns...
mergeBoxplotStats.listMerges a list of boxplot.stats() elements
nbrOfArrays.ChromosomalModelGets the number of arrays
nbrOfArrays.ExplorerGets the total number of arrays
nbrOfChipTypes.AromaMicroarrayDataSetTupleGets the number of chip types
nbrOfChipTypes.ChromosomalModelGets the number of chip types
Non-documented_objectsNon-documented objects
NonPairedPSCNDataThe NonPairedPSCNData class
PairedPSCNDataThe PairedPSCNData class
ParametersInterfaceThe ParametersInterface class interface
plotTracks.PairedPSCNDataPlots parental specific copy numbers along the genome
process.AromaTransformProcesses the data set
process.ChromosomeExplorerGenerates image files, scripts and dynamic pages for the...
process.ExplorerGenerates image files, scripts and dynamic pages for the...
processTimeGets the running time of the R process and its children...
RawAlleleBFractionsThe RawAlleleBFractions class
RawCopyNumberModelThe RawCopyNumberModel class
RawCopyNumbersThe RawCopyNumbers class
RawGenomicSignalsThe RawGenomicSignals class
RawMirroredAlleleBFractionsThe RawMirroredAlleleBFractions class
RawSequenceReadsThe RawSequenceReads class
readFooter.AromaTabularBinaryFileReads the file footer in XML format into a named nested list
segmentByCBS.RawGenomicSignalsSegment copy numbers using the CBS method
segmentByGLAD.RawGenomicSignalsSegment copy numbers using the GLAD method
segmentByHaarSeg.RawGenomicSignalsSegment copy numbers using the HaarSeg method
segmentByMPCBS.RawGenomicSignalsSegment copy numbers using the multi-platform CBS (mpCBS)...
SegmentedAlleleBFractionsThe SegmentedAlleleBFractions class
SegmentedCopyNumbersThe SegmentedCopyNumbers class
SegmentedGenomicSignalsInterfaceThe SegmentedGenomicSignalsInterface class interface
setAlias.ExplorerSets the alias of the output set
setArrays.ChromosomeExplorerSets the arrays
setArrays.ExplorerSets the arrays
UnitAnnotationDataFileThe UnitAnnotationDataFile interface class
UnitNamesFileThe UnitNamesFile interface class
UnitTypesFileThe UnitTypesFile interface class
updateSetupExplorerFile.ChromosomeExplorerUpdates the Javascript file
writeDataFrame.AromaUnitSignalBinaryFileWrites the data file as a tab-delimited text file
writeDataFrame.AromaUnitSignalBinarySetWrites the data set as a tab-delimited text file
writeDataFrame.AromaUnitTabularBinaryFileWrites the data file as a tab-delimited text file
writeFooter.AromaTabularBinaryFileWrites a named nested list to the file footer in XML format
HenrikBengtsson/aroma.core documentation built on May 30, 2018, 8:07 a.m.