AromaUnitFracBCnBinarySet: The AromaUnitFracBCnBinarySet class

Description

Package: aroma.core Class AromaUnitFracBCnBinarySet

Object ~~| ~~+--FullNameInterface ~~~~~~~| ~~~~~~~+--GenericDataFileSet ~~~~~~~~~~~~| ~~~~~~~~~~~~+--GenericTabularFileSet ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--AromaTabularBinarySet ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitSignalBinarySet ~~~~~~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~~~~~~+--AromaUnitFracBCnBinarySet

Directly known subclasses:

public static class AromaUnitFracBCnBinarySet extends AromaUnitSignalBinarySet

An AromaUnitFracBCnBinarySet object represents a set of AromaUnitFracBCnBinaryFiles with identical chip types.

Usage

AromaUnitFracBCnBinarySet(...)

Arguments

...

Arguments passed to AromaUnitSignalBinarySet.

Fields and Methods

Methods:

	`byName`
-
`writeDataFrame`	-

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

Details

The term "allele B fraction" is also know as "allele B frequency", which was coined by Peiffer et al. (2006). Note that the term "frequency" is a bit misleading since it is not a frequency in neither the statistical nor the population sense, but rather only proportion relative to the total amount of allele A and allele B signals, which is calculated for each sample independently.

References

[1] Peiffer et al., High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping, Genome Res, 2006.