AromaUnitPscnBinaryFile: The AromaUnitPscnBinaryFile class

Description

Package: aroma.core Class AromaUnitPscnBinaryFile

Object ~~| ~~+--FullNameInterface ~~~~~~~| ~~~~~~~+--GenericDataFile ~~~~~~~~~~~~| ~~~~~~~~~~~~+--ColumnNamesInterface ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--GenericTabularFile ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--CacheKeyInterface ~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~+--FileCacheKeyInterface ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaTabularBinaryFile ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaPlatformInterface ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinaryFile ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CopyNumberDataFile ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitPscnBinaryFile

Directly known subclasses:

public abstract static class AromaUnitPscnBinaryFile extends CopyNumberDataFile

An AromaUnitPscnBinaryFile is a AromaUnitSignalBinaryFile that holds total copy number signals (TCNs) and allele B fractions (BAFs). The TCNs can either be on an unknown scale or ratios relative to a reference. The signals are always stored on the original scale, i.e. they are never stored on the logaritmic scale. The BAFs are always on a [0-eps,1+eps] scale, where eps >= 0.

Usage

AromaUnitPscnBinaryFile(...)

Arguments

...

Arguments passed to AromaUnitSignalBinaryFile.

Fields and Methods

Methods:

	`extractRawCopyNumbers`
-
`hasAlleleBFractions`	-
	`hasStrandiness`
-
`hasTotalCopyNumberRatios`	-

Methods inherited from CopyNumberDataFile: as, as.CopyNumberDataFile, getNumberOfFilesAveraged, hasAlleleBFractions, hasStrandiness Methods inherited from AromaUnitSignalBinaryFile: allocate, allocateFromUnitAnnotationDataFile, allocateFromUnitNamesFile, as.character, extractMatrix, extractRawGenomicSignals, fromFile, getChipType, getExtensionPattern, getFilenameExtension, getNumberOfFilesAveraged, getPlatform, isAverageFile, nbrOfUnits, readDataFrame, writeDataFrame Methods inherited from AromaPlatformInterface: getAromaPlatform, getAromaUflFile, getAromaUgpFile, getChipType, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile, isCompatibleWith Methods inherited from AromaTabularBinaryFile: [, [<-, [[, allocate, as.character, colApply, colMeans, colStats, colSums, dimnames<-, getBytesPerColumn, getColClasses, getDefaultColumnNames, getRootName, importFrom, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, readFooter, readHeader, readRawFooter, setAttributesByTags, subset, summary, updateData, updateDataColumn, writeFooter, writeRawFooter Methods inherited from FileCacheKeyInterface: getCacheKey Methods inherited from CacheKeyInterface: getCacheKey Methods inherited from GenericTabularFile: [, as.character, dim, extractMatrix, head, nbrOfColumns, nbrOfRows, readColumns, readDataFrame, tail, writeColumnsToFiles Methods inherited from ColumnNamesInterface: appendColumnNamesTranslator, appendColumnNamesTranslatorByNULL, appendColumnNamesTranslatorBycharacter, appendColumnNamesTranslatorByfunction, appendColumnNamesTranslatorBylist, clearColumnNamesTranslator, clearListOfColumnNamesTranslators, getColumnNames, getColumnNamesTranslator, getDefaultColumnNames, getListOfColumnNamesTranslators, nbrOfColumns, setColumnNames, setColumnNamesTranslator, setListOfColumnNamesTranslators, updateColumnNames Methods inherited from GenericDataFile: as.character, clone, compareChecksum, copyTo, equals, fromFile, getAttribute, getAttributes, getChecksum, getChecksumFile, getCreatedOn, getDefaultFullName, getExtension, getExtensionPattern, getFileSize, getFileType, getFilename, getFilenameExtension, getLastAccessedOn, getLastModifiedOn, getOutputExtension, getPath, getPathname, gunzip, gzip, hasBeenModified, is.na, isFile, isGzipped, linkTo, readChecksum, renameTo, renameToUpperCaseExt, setAttribute, setAttributes, setAttributesBy, setAttributesByTags, setExtensionPattern, testAttributes, validate, validateChecksum, writeChecksum, getParentName Methods inherited from FullNameInterface: appendFullNameTranslator, appendFullNameTranslatorByNULL, appendFullNameTranslatorByTabularTextFile, appendFullNameTranslatorByTabularTextFileSet, appendFullNameTranslatorBycharacter, appendFullNameTranslatorBydata.frame, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, clearFullNameTranslator, clearListOfFullNameTranslators, getDefaultFullName, getFullName, getFullNameTranslator, getListOfFullNameTranslators, getName, getTags, hasTag, hasTags, resetFullName, setFullName, setFullNameTranslator, setListOfFullNameTranslators, setName, setTags, updateFullName Methods inherited from Object: $, $<-, [[, [[<-, as.character, attach, attachLocally, clearCache, clearLookupCache, clone, detach, equals, extend, finalize, getEnvironment, getFieldModifier, getFieldModifiers, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, save, asThis