ChipEffectSet {aroma.affymetrix}R Documentation

The ChipEffectSet class

Description

Package: aroma.affymetrix
Class ChipEffectSet

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

Directly known subclasses:
CnChipEffectSet, ExonChipEffectSet, SnpChipEffectSet

public static class ChipEffectSet
extends ParameterCelSet

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

Usage

ChipEffectSet(..., probeModel=c("pm"))

Arguments

... Arguments passed to AffymetrixCelSet.
probeModel The specific type of model, e.g. "pm".

Fields and Methods

Methods:
boxplotStats -
calculateBaseline Estimates the baseline signal chromosome by chromosome.
calculateFieldBoxplotStats -
calculateNuseBoxplotStats -
calculateRleBoxplotStats -
extractChromosomalDataFrame -
extractMatrix -
extractTheta -
findByName -
findUnitsTodo -
fromDataSet -
getAM Gets the log-intensities and log-ratios of chip effects of the set relative to a reference chip effect file.
getAverageFile -
getBaseline Gets the baseline signals across chromosomes.
getCellIndices -
getParameters -
getXAM Gets the physical position, log-intensities and log-ratios of chip effects for two arrays.
plotBoxplot -
readUnits -

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/)

See Also

An object of this class is typically obtained through the getChipEffectSet() method for the ProbeLevelModel class.


[Package aroma.affymetrix version 1.2.0 Index]