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