Package: aroma.affymetrix
Class FragmentEquivalentClassNormalization
Object
~~|
~~+--ParametersInterface
~~~~~~~|
~~~~~~~+--AromaTransform
~~~~~~~~~~~~|
~~~~~~~~~~~~+--Transform
~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~+--ChipEffectTransform
~~~~~~~~~~~~~~~~~~~~~~|
~~~~~~~~~~~~~~~~~~~~~~+--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.
FragmentEquivalentClassNormalization(dataSet=NULL, ..., targetAvgs=NULL,
subsetToFit="-XY")
A CnChipEffectSet.
Additional arguments passed to the constructor of
ChipEffectTransform.
An optional list of functions.
For each enzyme there is one target averages to which all arrays
should be normalized to.
The units from which the normalization curve should
be estimated. If NULL, all are considered.
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
This class requires an UFC (Unit Fragment Class) annotation file.
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.
Henrik Bengtsson