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