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aroma.core (version 1.3.1)

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: rll{ byName - exportFracBDiffSet - } Methods inherited from AromaUnitSignalBinarySet: byName, findByName, getAromaUgpFile, getChipType, getPlatform, validate Methods inherited from GenericTabularFileSet: calculateAverageColumnAcrossFiles, extractMatrix Methods inherited from GenericDataFileSet: append, appendFiles, appendFullNamesTranslator, appendFullNamesTranslatorByfunction, appendFullNamesTranslatorBylist, appendFullNamesTranslatorByNULL, as.list, byName, byPath, clearCache, clearFullNamesTranslator, copyTo, equals, extract, findByName, fromFiles, getAlias, getDefaultFullName, getFile, getFileClass, getFileSize, getFullNames, getNames, getPath, getPathnames, hasFile, indexOf, lapply, nbrOfFiles, sapply, seq, setAlias, setFullNamesTranslator, update2, updateFullName, updateFullNames, validate Methods inherited from FullNameInterface: appendFullNameTranslator, appendFullNameTranslatorBycharacter, appendFullNameTranslatorByfunction, appendFullNameTranslatorBylist, appendFullNameTranslatorByNULL, 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, clone, detach, equals, extend, finalize, gc, getEnvironment, getFields, getInstantiationTime, getStaticInstance, hasField, hashCode, ll, load, objectSize, print, registerFinalizer, save

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.