FragmentEquivalentClassNormalization {aroma.affymetrix} | R Documentation |
The FragmentEquivalentClassNormalization class
Description
Package: aroma.affymetrix
Class FragmentEquivalentClassNormalization
Object
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ParametersInterface
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AromaTransform
~~~~~~~~~~~~|
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Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--
ChipEffectTransform
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FragmentEquivalentClassNormalization
Directly known subclasses:
public static class FragmentEquivalentClassNormalization
extends ChipEffectTransform
This class represents a normalization method that corrects for systematic effects between loci of different equivalent classes of pairs of sequences that are recognized by the restriction enzymes that cut the DNA studies.
Usage
FragmentEquivalentClassNormalization(dataSet=NULL, ..., targetAvgs=NULL,
subsetToFit="-XY")
Arguments
dataSet |
|
... |
Additional arguments passed to the constructor of
|
targetAvgs |
An optional list of |
subsetToFit |
The units from which the normalization curve should
be estimated. If |
Fields and Methods
Methods:
getAromaUfcFile | - | |
getCdf | - | |
process | - | |
Methods inherited from ChipEffectTransform:
getRootPath
Methods inherited from Transform:
getOutputDataSet, getOutputFiles
Methods inherited from AromaTransform:
as.character, findFilesTodo, getAsteriskTags, getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getRootPath, getTags, isDone, process, setTags
Methods inherited from ParametersInterface:
getParameterSets, getParameters, getParametersAsString
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
Requirements
This class requires an UFC (Unit Fragment Class) annotation file.
Acknowledgments
The idea of normalization signals stratified on enzyme recognition sequences is credited to Jim Veitch and Ben Bolstad at Affymetrix Inc. (2008) who have designed a similar method for copy number estimation in the Affymetrix' Genotype Console v2.
Author(s)
Henrik Bengtsson