The AromaPlatform class
AromaMicroarrayTabularBinaryFile
The AromaMicroarrayTabularBinaryFile class
The UnitTypesFile interface class
The AromaUnitCallSet class
The AromaUnitCallFile class
getTableOfArrays.AromaMicroarrayDataSetTuple
Gets a table of arrays
The AromaMicroarrayDataSet class
Gets the alias of the output set
estimateStandardDeviation.RawGenomicSignals
Estimates the standard deviation of the raw Ys
allocate.AromaTabularBinaryFile
Creates an AromaTabularBinaryFile
The UnitNamesFile interface class
Non-documented objects
The RawGenomicSignals class
The abstract AromaMicroarrayDataFile class
SegmentedAlleleBFractions
The SegmentedAlleleBFractions class
The RawSequenceReads class
segmentByHaarSeg.RawGenomicSignals
Segment copy numbers using the HaarSeg method
Locates an annotation data file
getArrayTuple.AromaMicroarrayDataSetTuple
Gets arrays across chip types for one sample
Gets the name of the explorer
RawMirroredAlleleBFractions
The RawMirroredAlleleBFractions class
The AromaTransform class
AromaUnitGenotypeCallFile
The AromaUnitGenotypeCallFile class
Gets the running time of the R process and its children processes
nbrOfArrays.AromaMicroarrayDataSetTuple
Gets the number of arrays
AromaUnitSignalBinaryFile
The AromaUnitSignalBinaryFile class
The AromaUnitGenotypeCallSet class
The UnitAnnotationDataFile interface class
Merges a list of boxplot.stats() elements
AromaUnitTabularBinaryFile
The AromaUnitTabularBinaryFile class
Creates a Grayscale (TrueColor) Image from a matrix file
SegmentedGenomicSignalsInterface
The SegmentedGenomicSignalsInterface class interface
AromaCellTabularBinaryFile
The AromaCellTabularBinaryFile class
Gets the name of the output data set
Gets the path of the output data set
AromaUnitFracBCnBinaryFile
The AromaUnitFracBCnBinaryFile class
Gets the names of the arrays
The SegmentedCopyNumbers class
AromaUnitTotalCnBinaryFile
The AromaUnitTotalCnBinaryFile class
Gets the tags of the output data set
The AromaTabularBinarySet class
Displays the explorer in the default browser
Download a package patch
colBinnedSmoothing.matrix
Binned smoothing of a matrix column by column
fitGenotypeConeBySfit.matrix
Fits an affine transformation to allele A and allele B data
AromaUnitFracBCnBinarySet
The AromaUnitFracBCnBinarySet class
getArrays.AromaMicroarrayDataSetTuple
Gets the names of the arrays
colKernelSmoothing.matrix
Kernel smoothing of a matrix column by column
The AromaTabularBinaryFile class
Package aroma.core
The RawCopyNumbers class
The RawAlleleBFractions class
AromaMicroarrayDataSetTuple
The AromaMicroarrayDataSetTuple class
Applies a polishing function to blocks of rows and columns repeatedly
writeFooter.AromaTabularBinaryFile
Writes a named nested list to the file footer in XML format
Processes the data set
Checks if the data set is processed or not
fitMultiDimensionalCone.matrix
Fits an affine transformation to multi-dimensional data
getInputDataSet.AromaTransform
Gets the input data set
Fits an affine transformation to allele A and allele B data
The BinnedScatter class
Sets the alias of the output set
readFooter.AromaTabularBinaryFile
Reads the file footer in XML format into a named nested list
getFullName.AromaTransform
Gets the full name of the output data set
The AromaUnitSignalBinarySet class
AromaUnitTotalCnBinarySet
The AromaUnitTotalCnBinarySet class
The AromaUnitTypesFile class
segmentByGLAD.RawGenomicSignals
Segment copy numbers using the GLAD method
Generates image files, scripts and dynamic pages for the explorer
The Explorer class
extract.AromaMicroarrayDataSetTuple
Extracts a subset AromaMicroarrayDataSetTuple
segmentByCBS.RawGenomicSignals
Segment copy numbers using the CBS method
getOutputDataSet.AromaTransform
Gets the transformed data set
Gets the tags of the explorer
indexOfArrays.AromaMicroarrayDataSetTuple
Gets the indices of the arrays
Gets the indices of units by their names
nbrOfChipTypes.AromaMicroarrayDataSetTuple
Gets the number of chip types
findAnnotationDataByChipType
Locates an annotation data file by its chip type
Gets the total number of arrays
Applies patches for a specific package
Sets the arrays