GcContentNormalization {aroma.affymetrix}R Documentation

The GcContentNormalization class

Description

Package: aroma.affymetrix
Class GcContentNormalization

Object
~~|
~~+--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 -
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, save

Requirements

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

Author(s)

Henrik Bengtsson (http://www.braju.com/R/)


[Package aroma.affymetrix version 1.2.0 Index]