FragmentEquivalentClassNormalization: The FragmentEquivalentClassNormalization class

Description

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.

Usage

FragmentEquivalentClassNormalization(dataSet=NULL, ..., targetAvgs=NULL, subsetToFit="-XY")

Arguments

dataSet

A CnChipEffectSet.

...

Additional arguments passed to the constructor of ChipEffectTransform.

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:

	`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, 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.