aroma.core (version 2.7.0)

AromaUnitPscnBinaryFile: The AromaUnitPscnBinaryFile class

Description

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