CnChipEffectSet {aroma.affymetrix}R Documentation

The CnChipEffectSet class

Description

Package: aroma.affymetrix
Class CnChipEffectSet

Object
~~|
~~+--GenericDataFileSet
~~~~~~~|
~~~~~~~+--AromaMicroarrayDataSet
~~~~~~~~~~~~|
~~~~~~~~~~~~+--AromaPlatformInterface
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--AffymetrixFileSet
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--AffymetrixCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ParameterCelSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--ChipEffectSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--SnpChipEffectSet
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~+--CnChipEffectSet

Directly known subclasses:

public static class CnChipEffectSet
extends SnpChipEffectSet

This class represents estimates of chip effects in the probe-level models.

Usage

CnChipEffectSet(..., combineAlleles="byFirstFile")

Arguments

... Arguments passed to SnpChipEffectSet.
combineAlleles A logical indicating if the signals from allele A and allele B are combined or not.

Fields and Methods

Methods:
exportTotalAndFracB -
extractTheta -
extractTotalAndFreqB -
getAverageFile -
getBaseline -
getCombineAlleles -
setCombineAlleles -
writeWig -

Methods inherited from SnpChipEffectSet:
exportTotalAndFracB, extractCNT, extractSnpCnvQSet, extractSnpQSet, extractTheta, extractTotalAndFreqB, fromFiles, getAverageFile, getBaseline, getMergeStrands, setMergeStrands, writeCNT

Methods inherited from ChipEffectSet:
boxplotStats, calculateBaseline, calculateFieldBoxplotStats, calculateNuseBoxplotStats, calculateRleBoxplotStats, extractChromosomalDataFrame, extractMatrix, extractTheta, findByName, findUnitsTodo, fromDataSet, fromFiles, getAM, getAsFullCelSet, getAverageFile, getBaseline, getCellIndices, getParameters, getXAM, plotBoxplot, readUnits, updateUnits

Methods inherited from ParameterCelSet:
extractDataFrame, extractMatrix

Methods inherited from AffymetrixCelSet:
[, [[, append, as, as.AffymetrixCelSet, averageQuantile, byName, convertToUnique, extractAffyBatch, extractMatrix, findByName, fromFiles, getAverage, getAverageAsinh, getAverageFile, getAverageLog, getCdf, getChipType, getData, getFullName, getIntensities, getPlatform, getTimestamps, getUnitGroupCellMap, getUnitIntensities, getUnitNamesFile, getUnitTypesFile, isDuplicated, justSNPRMA, nbrOfArrays, normalizeQuantile, plotDensity, range, readUnits, setCdf, update2, writeSgr

Methods inherited from AffymetrixFileSet:
as, as.AffymetrixFileSet, fromFiles

Methods inherited from AromaPlatformInterface:
getAromaPlatform, getPlatform, getUnitAnnotationDataFile, getUnitNamesFile, getUnitTypesFile

Methods inherited from AromaMicroarrayDataSet:
getChipType, getPlatform, nbrOfArrays, setAttributesBy, setAttributesBySampleAnnotationFile, setAttributesBySampleAnnotationSet, validate

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, registerFinalizer, save

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)


[Package aroma.affymetrix version 1.2.0 Index]