aroma.core v3.1.1

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Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

Core methods and classes used by higher-level aroma.* packages part of the Aroma Project, e.g. aroma.affymetrix and aroma.cn.

Functions in aroma.core

Name Description
AromaCellTabularBinaryFile The AromaCellTabularBinaryFile class
AromaGenomeTextFile The AromaGenomeTextFile class
AbstractCNData The AbstractCNData class
AbstractPSCNData The AbstractPSCNData class
AromaMicroarrayDataFile The abstract AromaMicroarrayDataFile class
AromaMicroarrayDataSet The AromaMicroarrayDataSet class
AromaMicroarrayDataSetTuple The AromaMicroarrayDataSetTuple class
AromaMicroarrayTabularBinaryFile The AromaMicroarrayTabularBinaryFile class
AromaCellCpgFile A binary file holding local CpG density for each cell (probe/feature)
AromaCellPositionFile A binary file holding chromosome/position for each cell
AromaPlatform The AromaPlatform class
AromaPlatformInterface The AromaPlatformInterface class
AromaTabularBinarySet The AromaTabularBinarySet class
AromaTransform The AromaTransform class
AromaRepository The AromaRepository class
AromaTabularBinaryFile The AromaTabularBinaryFile class
AromaUnitTabularBinaryFile The AromaUnitTabularBinaryFile class
AromaUnitTotalCnBinaryFile The AromaUnitTotalCnBinaryFile class
AromaUnitCallFile The AromaUnitCallFile class
AromaUnitCallSet The AromaUnitCallSet class
AromaUnitSignalBinaryFile The AromaUnitSignalBinaryFile class
AromaUnitSignalBinarySet The AromaUnitSignalBinarySet class
AromaUnitTotalCnBinarySet The AromaUnitTotalCnBinarySet class
AromaUnitTypesFile The AromaUnitTypesFile class
BinnedScatter The BinnedScatter class
CacheKeyInterface The CacheKeyInterface class interface
NonPairedPSCNData The NonPairedPSCNData class
AromaUnitPscnBinaryFile The AromaUnitPscnBinaryFile class
AromaUnitPscnBinarySet The AromaUnitPscnBinarySet class
FileCacheKeyInterface The FileCacheKeyInterface class interface
GladModel The GladModel class
PairedPSCNData The PairedPSCNData class
UnitAnnotationDataFile The UnitAnnotationDataFile interface class
UnitNamesFile The UnitNamesFile interface class
RawCopyNumberModel The RawCopyNumberModel class
RawCopyNumbers The RawCopyNumbers class
aroma.core-package Package aroma.core
as.GrayscaleImage.matrix Creates a Grayscale (Color) Image from a matrix file
CopyNumberSegmentationModel The CopyNumberSegmentationModel class
Explorer The Explorer class
RawGenomicSignals The RawGenomicSignals class
AromaUnitFracBCnBinaryFile The AromaUnitFracBCnBinaryFile class
AromaUnitFracBCnBinarySet The AromaUnitFracBCnBinarySet class
AromaUnitGenotypeCallFile The AromaUnitGenotypeCallFile class
AromaUnitGenotypeCallSet The AromaUnitGenotypeCallSet class
CbsModel The CbsModel class
colBinnedSmoothing.matrix Binned smoothing of a matrix column by column
colKernelSmoothing.matrix Kernel smoothing of a matrix column by column
findAnnotationData Locates an annotation data file
findAnnotationDataByChipType Locates an annotation data file by its chip type
getChipType.AromaPlatformInterface Gets the chip type
ChromosomeExplorer The ChromosomeExplorer class
CopyNumberChromosomalModel The CopyNumberChromosomalModel class
HaarSegModel The HaarSegModel class
Non-documented objects Non-documented objects
SegmentedCopyNumbers The SegmentedCopyNumbers class
SegmentedGenomicSignalsInterface The SegmentedGenomicSignalsInterface class interface
exportAromaUnitPscnBinarySet Export total and allele B signal data sets as a unified parent-specific copy number signal data set
extractRawCopyNumbers.CopyNumberChromosomalModel Extracts relative copy numbers
fitGenotypeConeBySfit.matrix Fits an affine transformation to allele A and allele B data
fitMultiDimensionalCone.matrix Fits an affine transformation to multi-dimensional data
getChromosomes.ChromosomalModel Gets the chromosomes to be processed
ChromosomalModel The ChromosomalModel class
ParametersInterface The ParametersInterface class interface
RawAlleleBFractions The RawAlleleBFractions class
UnitTypesFile The UnitTypesFile interface class
AromaTabularBinaryFile$allocate Creates an AromaTabularBinaryFile
downloadChipTypeFile.AromaRepository Download a particular chip type annotation file
downloadFile.AromaRepository Download a particular file from the reposity
getChipType.ChromosomalModel Gets a label for all chip types merged
getPath.AromaTransform Gets the path of the output directory
getPath.Explorer Gets the path of the output directory
indexOf.UnitNamesFile Gets the indices of units by their names
isCompatibleWith.AromaPlatformInterface Checks if a particular unit annotation data file is compatible
RawMirroredAlleleBFractions The RawMirroredAlleleBFractions class
getChromosomes.ChromosomeExplorer Gets the chromosomes available
getNames.Explorer Gets the names of the input samples
getOutputDataSet.AromaTransform Gets the transformed data set
isDone.AromaTransform Checks if the data set is processed or not
listFiles.AromaRepository Retrieves the files available on the repository under a particular path
process.ChromosomeExplorer Generates image files, scripts and dynamic pages for the explorer
process.Explorer Generates image files, scripts and dynamic pages for the explorer
setArrays.Explorer Sets the arrays
nbrOfArrays.ChromosomalModel Gets the number of arrays
nbrOfArrays.Explorer Gets the total number of arrays
writeDataFrame.AromaUnitSignalBinaryFile Writes the data file as a tab-delimited text file
writeDataFrame.AromaUnitSignalBinarySet Writes the data set as a tab-delimited text file
display.Explorer Displays the explorer in the default browser
doCBS Performs Circular Binary Segmentation (CBS) on a data set
fit.CopyNumberSegmentationModel Fits the model
fitGenotypeCone.matrix Fits an affine transformation to allele A and allele B data
getFullName.AromaTransform Gets the full name of the output data set
getInputDataSet.AromaTransform Gets the input data set
getPlatform.AromaPlatformInterface Gets the platform
getRootPath.AromaTransform Gets the root path of the output directory
findFilesTodo.AromaTransform Finds files in the data set still not processed
fit.CopyNumberChromosomalModel Fits the model
getCacheKey.CacheKeyInterface Gets a list of cache key items
matrixBlockPolish.matrix Applies a polishing function to blocks of rows and columns repeatedly
mergeBoxplotStats.list Merges a list of boxplot.stats() elements
nbrOfChipTypes.AromaMicroarrayDataSetTuple Gets the number of chip types
nbrOfChipTypes.ChromosomalModel Gets the number of chip types
updateSetupExplorerFile.ChromosomeExplorer Updates the Javascript file
RawSequenceReads The RawSequenceReads class
SegmentedAlleleBFractions The SegmentedAlleleBFractions class
estimateSds.CopyNumberChromosomalModel Estimates the standard deviation of the raw copy numbers (log2-ratios) robustly
estimateStandardDeviation.RawGenomicSignals Estimates the standard deviation of the raw Ys
getCacheKey.FileCacheKeyInterface Gets a list of cache key items
getParameters.ParametersInterface Gets a list of parameters
getParametersAsString.ParametersInterface Gets the parameters as character
getTags.Explorer Gets the tags of the explorer
getUnitAnnotationDataFile.AromaPlatformInterface Gets a unit annotation data file of a particular class
segmentByHaarSeg.RawGenomicSignals Segment copy numbers using the HaarSeg method
segmentByMPCBS.RawGenomicSignals Segment copy numbers using the multi-platform CBS (mpCBS) method
getAlias.Explorer Gets the alias of the output set
getAromaPlatform.AromaPlatformInterface Gets the platform
getModel.ChromosomeExplorer Gets the model
getName.AromaTransform Gets the name of the output data set
getName.Explorer Gets the name of the explorer
plotTracks.PairedPSCNData Plots parental specific copy numbers along the genome
process.AromaTransform Processes the data set
segmentByCBS.RawGenomicSignals Segment copy numbers using the CBS method
getNames.ChromosomalModel Gets the names of the arrays
getRootPath.Explorer Gets the root path of the output directory
getTags.AromaTransform Gets the tags of the output data set
processTime 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
segmentByGLAD.RawGenomicSignals Segment copy numbers using the GLAD method
setAlias.Explorer Sets the alias of the output set
setArrays.ChromosomeExplorer Sets the arrays
writeDataFrame.AromaUnitTabularBinaryFile Writes the data file as a tab-delimited text file
writeFooter.AromaTabularBinaryFile Writes a named nested list to the file footer in XML format
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DependsNote BioC (>= 3.0)
SuggestsNote BioC (>= 3.0), Recommended: aroma.light, DNAcopy, png, preprocessCore, sfit
Additional_repositories http://r-forge.r-project.org, https://henrikbengtsson.github.io/drat
Date 2017-09-12
License LGPL (>= 2.1)
URL https://github.com/HenrikBengtsson/aroma.core, http://www.aroma-project.org/
BugReports https://github.com/HenrikBengtsson/aroma.core/issues
LazyLoad TRUE
biocViews Microarray, OneChannel, TwoChannel, MultiChannel, DataImport, DataRepresentation, GUI, Visualization, Preprocessing, QualityControl, aCGH, CopyNumberVariants
RoxygenNote 6.0.1
NeedsCompilation no
Packaged 2017-09-12 22:12:36 UTC; hb
Repository CRAN
Date/Publication 2017-09-13 07:24:30 UTC

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