GcContentNormalization: The GcContentNormalization class

In HenrikBengtsson/aroma.affymetrix: Analysis of Large Affymetrix Microarray Data Sets

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, names, objectSize, print, save, asThis

Requirements

This class requires an Aroma unit GC-content (UGC) file.

Author(s)

Henrik Bengtsson

HenrikBengtsson/aroma.affymetrix documentation built on Feb. 20, 2024, 9:07 p.m.