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.AromaUnitTotalCnBinarySet(...)AromaUnitSignalBinarySet.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, na.omit, names, nbrOfFiles, rep, resetFullNames, seq, 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