AromaUnitTotalCnBinarySet: The AromaUnitTotalCnBinarySet class

Description

Package: aroma.core Class AromaUnitTotalCnBinarySet

Object ~~| ~~+--FullNameInterface ~~~~~~~| ~~~~~~~+--GenericDataFileSet ~~~~~~~~~~~~| ~~~~~~~~~~~~+--GenericTabularFileSet ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--AromaTabularBinarySet ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinarySet ~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CopyNumberDataSet ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitTotalCnBinarySet

Directly known subclasses:

public static class AromaUnitTotalCnBinarySet extends CopyNumberDataSet

An AromaUnitTotalCnBinarySet object represents a set of AromaUnitTotalCnBinaryFiles with identical chip types.

Usage

AromaUnitTotalCnBinarySet(...)

Arguments

...

Arguments passed to AromaUnitSignalBinarySet.

Fields and Methods

Methods:

	`as.AromaUnitTotalCnBinarySetTuple`
-
`as.CopyNumberDataSetTuple`	-
	`byName`
-
`exportAromaUnitPscnBinarySet`	-
	`exportTotalCnRatioSet`
-
`extractPSCNArray`	-
	`getAverageFile`
-
`getUnitNamesFile`	-
	`writeDataFrame`
-

Methods inherited from CopyNumberDataSet: as, as.CopyNumberDataSet, doCBS, hasAlleleBFractions, hasStrandiness Methods inherited from AromaUnitSignalBinarySet: byName, findByName, getAromaFullNameTranslatorSet, getAromaUgpFile, getChipType, getPlatform, validate, writeDataFrame Methods inherited from AromaTabularBinarySet: getDefaultFullName, getRootName, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, setAttributesByTags Methods inherited from GenericTabularFileSet: extractMatrix, calculateAverageColumnAcrossFiles Methods inherited from GenericDataFileSet: [, [[, anyDuplicated, anyNA, append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByNULL, appendFullNamesTranslatorByTabularTextFile, appendFullNamesTranslatorByTabularTextFileSet, appendFullNamesTranslatorBydata.frame, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, as.character, as.list, byName, byPath, c, clearCache, clearFullNamesTranslator, clone, copyTo, dsApply, dsApplyInPairs, duplicated, equals, extract, findByName, findDuplicated, getChecksum, getChecksumFileSet, getChecksumObjects, getDefaultFullName, getFile, getFileClass, getFileSize, getFiles, getFullNames, getNames, getOneFile, getPath, getPathnames, getSubdirs, gunzip, gzip, hasFile, indexOf, is.na, names, nbrOfFiles, rep, resetFullNames, setFullNamesTranslator, sortBy, unique, update2, updateFullName, updateFullNames, validate, getFullNameTranslatorSet, 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