aroma.affymetrix (version 3.0.0)

GcContentNormalization: The GcContentNormalization class

Description

Package: aroma.affymetrix Class GcContentNormalization

Object ~~| ~~+--ParametersInterface ~~~~~~~| ~~~~~~~+--AromaTransform ~~~~~~~~~~~~| ~~~~~~~~~~~~+--Transform ~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~+--ChipEffectTransform ~~~~~~~~~~~~~~~~~~~~~~| ~~~~~~~~~~~~~~~~~~~~~~+--GcContentNormalization

Directly known subclasses:

public static class GcContentNormalization extends ChipEffectTransform

Usage

GcContentNormalization(dataSet=NULL, ..., targetFunction=NULL, subsetToFit=NULL)

Arguments

dataSet

A CnChipEffectSet.

...

Additional arguments passed to the constructor of ChipEffectTransform.

targetFunction

A function. The target function 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:

	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 Aroma unit GC-content (UGC) file.