Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework
Performs Circular Binary Segmentation (CBS) on a data set
Download a particular chip type annotation file
Download a particular file from the repository
Estimates the standard deviation of the raw copy numbers (log2-ratios)...
Estimates the standard deviation of the raw Ys
The CopyNumberSegmentationModel class
Displays the explorer in the default browser
The AbstractCNData class
The AbstractPSCNData class
Creates an AromaTabularBinaryFile
Package aroma.core
A binary file holding local CpG density for each cell (probe/feature)
A binary file holding chromosome/position for each cell
The AromaCellTabularBinaryFile class
The AromaGenomeTextFile class
The abstract AromaMicroarrayDataFile class
The AromaMicroarrayDataSet class
The AromaMicroarrayDataSetTuple class
The AromaMicroarrayTabularBinaryFile class
The AromaPlatform class
The AromaPlatformInterface class
The AromaRepository class
The AromaTabularBinaryFile class
The AromaTabularBinarySet class
The AromaTransform class
The AromaUnitCallFile class
The AromaUnitCallSet class
The AromaUnitFracBCnBinaryFile class
The AromaUnitFracBCnBinarySet class
The AromaUnitGenotypeCallFile class
The AromaUnitGenotypeCallSet class
The AromaUnitPscnBinaryFile class
The AromaUnitPscnBinarySet class
The AromaUnitSignalBinaryFile class
The AromaUnitSignalBinarySet class
The AromaUnitTabularBinaryFile class
The AromaUnitTotalCnBinaryFile class
The AromaUnitTotalCnBinarySet class
The AromaUnitTypesFile class
Creates a Grayscale (Color) Image from a matrix file
The BinnedScatter class
The CacheKeyInterface class interface
The CbsModel class
The ChromosomalModel class
The ChromosomeExplorer class
Binned smoothing of a matrix column by column
Kernel smoothing of a matrix column by column
The CopyNumberChromosomalModel class
The Explorer class
Export total and allele B signal data sets as a unified parent-specifi...
Extracts relative copy numbers
The FileCacheKeyInterface class interface
Locates an annotation data file
Locates an annotation data file by its chip type
Finds files in the data set still not processed
Fits the model
Fits the model
Fits an affine transformation to allele A and allele B data
Fits an affine transformation to allele A and allele B data
Fits an affine transformation to multi-dimensional data
Gets the alias of the output set
Gets the platform
Gets a list of cache key items
Gets a list of cache key items
Gets the chip type
Gets a label for all chip types merged
Gets the chromosomes to be processed
Gets the chromosomes available
Gets the full name of the output data set
Gets the input data set
Gets the model
Gets the name of the output data set
Gets the name of the explorer
Gets the names of the arrays
Gets the names of the input samples
Gets the transformed data set
Gets a list of parameters
Gets the parameters as character
Gets the path of the output directory
Gets the path of the output directory
Gets the platform
Gets the root path of the output directory
Gets the root path of the output directory
Gets the tags of the output data set
Gets the tags of the explorer
Gets a unit annotation data file of a particular class
The GladModel class
The HaarSegModel class
Gets the indices of units by their names
Checks if a particular unit annotation data file is compatible
Checks if the data set is processed or not
Retrieves the files available on the repository under a particular pat...
Applies a polishing function to blocks of rows and columns repeatedly
Merges a list of boxplot.stats() elements
Gets the number of arrays
Gets the total number of arrays
Gets the number of chip types
Gets the number of chip types
Non-documented objects
The NonPairedPSCNData class
The PairedPSCNData class
The ParametersInterface class interface
Plots parental specific copy numbers along the genome
Processes the data set
Generates image files, scripts and dynamic pages for the explorer
Generates image files, scripts and dynamic pages for the explorer
Gets the running time of the R process and its children processes
The RawAlleleBFractions class
The RawCopyNumberModel class
The RawCopyNumbers class
The RawGenomicSignals class
The RawMirroredAlleleBFractions class
The RawSequenceReads class
Reads the file footer in XML format into a named nested list
Segment copy numbers using the CBS method
Segment copy numbers using the GLAD method
Segment copy numbers using the HaarSeg method
Segment copy numbers using the multi-platform CBS (mpCBS) method
The SegmentedAlleleBFractions class
The SegmentedCopyNumbers class
The SegmentedGenomicSignalsInterface class interface
Sets the alias of the output set
Sets the arrays
Sets the arrays
The UnitAnnotationDataFile interface class
The UnitNamesFile interface class
The UnitTypesFile interface class
Updates the Javascript file
Writes the data file as a tab-delimited text file
Writes the data set as a tab-delimited text file
Writes the data file as a tab-delimited text file
Writes a named nested list to the file footer in XML format
Core methods and classes used by higher-level 'aroma.*' packages part of the Aroma Project, e.g. 'aroma.affymetrix' and 'aroma.cn'.
Useful links