FragmentEquivalentClassNormalization: The FragmentEquivalentClassNormalization class
Description
Package: aroma.affymetrix
Class FragmentEquivalentClassNormalization
Object
~~|
~~+--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.Usage
FragmentEquivalentClassNormalization(dataSet=NULL, ..., targetAvgs=NULL, subsetToFit="-XY")
Arguments
targetAvgs
An optional list of functions.
For each enzyme there is one target averages to which all arrays
should be normalized to. subsetToFit
The units from which the normalization curve should
be estimated. If NULL, all are considered. Fields and Methods
Methods:
rll{
clearCache -
getAromaUfcFile -
getCdf -
getOutputDataSet00 -
process Normalizes the data set.
}
Methods inherited from Transform:
getOutputDataSet, getOutputDataSetOLD20090509, getOutputFiles
Methods inherited from AromaTransform:
getExpectedOutputFiles, getExpectedOutputFullnames, getFullName, getInputDataSet, getName, getOutputDataSet, getOutputDataSet0, getOutputFiles, getPath, getTags, isDone, process, setTags
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, saveRequirements
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.