AromaUnitFracBCnBinarySet: The AromaUnitFracBCnBinarySet class

In aroma.core: Core Methods and Classes Used by 'aroma.*' Packages Part of the Aroma Framework

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.

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.

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, 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, names, objectSize, print, save, asThis

Author(s)

Henrik Bengtsson

References

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

aroma.core documentation built on June 25, 2024, 1:15 a.m.