AromaUnitFracBCnBinarySet: The AromaUnitFracBCnBinarySet class

Description

Package: aroma.core Class AromaUnitFracBCnBinarySet Object ~~| ~~+--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, as.list, byName, clearCache, copyTo, equals, extract, findByName, fromFiles, getAlias, getFile, getFileClass, getFileSize, getFullName, getFullNames, getFullNameTranslator, getName, getNames, getPath, getPathnames, getTags, hasFile, hasTag, hasTags, indexOf, lapply, nbrOfFiles, sapply, seq, setAlias, setFullName, setFullNamesTranslator, setFullNameTranslator, setName, setTags, update2, validate 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, 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.