AbstractCurveNormalization

Package: aroma.cn 
Class AbstractCurveNormalization 
<code>Object</code> 
<code>~~|</code> 
<code>~~+--</code><code>AbstractCurveNormalization</code> 
Directly known subclasses: 
PrincipalCurveNormalization, XYCurveNormalization 
public abstract static class AbstractCurveNormalization 
extends Object

classes

Methods for analyzing DNA copy-number data.  Specifically,
this package implements the multi-source copy-number normalization (MSCN)
method for normalizing copy-number data obtained on various platforms and
technologies.  It also implements the TumorBoost method for normalizing
paired tumor-normal SNP data.

Henrik Bengtsson

aroma.cn

Copy-Number Analysis of Large Microarray Data Sets

Pierre Neuvial

AbstractCurveNormalization function

<dl> <dt>dataSet</dt>
<dd>An <code>AromaUnitTotalCnBinarySet</code> of
 "test" samples to be normalized.</dd> <dt>targetSet</dt>
<dd>An <code>AromaUnitTotalCnBinarySet</code> of
 paired target samples.</dd> <dt>subsetToFit</dt>
<dd>The subset of loci to be used to fit the
 normalization functions.
 If <code><a href="/link/NULL?package=aroma.cn&version=1.7.1" data-mini-rdoc="aroma.cn::NULL">NULL</a></code>, loci on chromosomes 1-22 are used, but not on ChrX and ChrY.</dd> <dt>tags</dt>
<dd>(Optional) Sets the tags for the output data sets.</dd> <dt>copyTarget</dt>
<dd>If <code><a href="/link/TRUE?package=aroma.cn&version=1.7.1" data-mini-rdoc="aroma.cn::TRUE">TRUE</a></code>, target arrays are copied to the output
 data set, otherwise not.</dd> <dt>...</dt>
<dd>Not used.</dd></dl>

Arguments

Methods: <table class="table">
<tr><td></td><td><code>getFullName</code></td><td>-</td></tr>
<tr><td></td><td><code>getInputDataSet</code></td><td>-</td></tr>
<tr><td></td><td><code>getName</code></td><td>-</td></tr>
<tr><td></td><td><code>getOutputDataSet</code></td><td>-</td></tr>
<tr><td></td><td><code>getTags</code></td><td>-</td></tr>
<tr><td></td><td><code>getTargetDataSet</code></td><td>-</td></tr>
<tr><td></td><td><code>process</code></td><td>-</td></tr>
<tr><td></td><td><code>setTags</code></td><td>-</td></tr>
</table>Methods inherited from Object: 
$, $&lt;-, [[, [[&lt;-, 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

Fields and Methods

Author

Package: aroma.cn 
Class AbstractCurveNormalization 
<code>Object</code> 
<code>~~|</code> 
<code>~~+--</code><code>AbstractCurveNormalization</code> 
Directly known subclasses: 
PrincipalCurveNormalization, XYCurveNormalization 
public abstract static class AbstractCurveNormalization 
extends Object

The AbstractCurveNormalization class — AbstractCurveNormalization

<dl>

 <dt>dataSet</dt>
<dd>An <code>AromaUnitTotalCnBinarySet</code> of
 "test" samples to be normalized.</dd>

 <dt>targetSet</dt>
<dd>An <code>AromaUnitTotalCnBinarySet</code> of
 paired target samples.</dd>

 <dt>subsetToFit</dt>
<dd>The subset of loci to be used to fit the
 normalization functions.
 If <code><a href='https://rdrr.io/r/base/NULL.html'>NULL</a></code>, loci on chromosomes 1-22 are used, but not on ChrX and ChrY.</dd>

 <dt>tags</dt>
<dd>(Optional) Sets the tags for the output data sets.</dd>

 <dt>copyTarget</dt>
<dd>If <code><a href='https://rdrr.io/r/base/logical.html'>TRUE</a></code>, target arrays are copied to the output
 data set, otherwise not.</dd>

 <dt>...</dt>
<dd>Not used.</dd>

</dl>

Methods: <table class='table'>
<tr><td></td><td><code>getFullName</code></td><td>-</td></tr>
<tr><td></td><td><code>getInputDataSet</code></td><td>-</td></tr>
<tr><td></td><td><code>getName</code></td><td>-</td></tr>
<tr><td></td><td><code>getOutputDataSet</code></td><td>-</td></tr>
<tr><td></td><td><code>getTags</code></td><td>-</td></tr>
<tr><td></td><td><code>getTargetDataSet</code></td><td>-</td></tr>
<tr><td></td><td><code>process</code></td><td>-</td></tr>
<tr><td></td><td><code>setTags</code></td><td>-</td></tr>
</table>



Methods inherited from Object: 
$, $&lt;-, [[, [[&lt;-, 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

	`getFullName`	-
	`getInputDataSet`	-
	`getName`	-
	`getOutputDataSet`	-
	`getTags`	-
	`getTargetDataSet`	-
	`process`	-
	`setTags`	-

AbstractCurveNormalization: The AbstractCurveNormalization class

Description

Usage

Arguments

Fields and Methods

Author