normalizePrincipalCurve.matrix

Normalizes data in K dimensions using principal curves such that afterward the data cluster (approximately
 linearly) along the diagonal (in K dimensions).

methods

internal

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

normalizePrincipalCurve.matrix function

<dl> <dt>x</dt>
<dd>An NxK <code><a href="/link/matrix?package=aroma.cn&version=1.6.1" data-mini-rdoc="aroma.cn::matrix">matrix</a></code> where the columns represent the
 (K &gt;= 2) dimensions.</dd> <dt>...</dt>
<dd>Additional arguments passed to
 <code>fitPrincipalCurve</code> used for fitting the model.</dd> <dt>center</dt>
<dd>If <code><a href="/link/TRUE?package=aroma.cn&version=1.6.1" data-mini-rdoc="aroma.cn::TRUE">TRUE</a></code>, normalized data is centered such that the median
 signal in each dimension is at zero.</dd> <dt>returnFit</dt>
<dd>If <code><a href="/link/TRUE?package=aroma.cn&version=1.6.1" data-mini-rdoc="aroma.cn::TRUE">TRUE</a></code>, the fitted principal curve parameters are
 returned as an attribute.</dd></dl>

Arguments

Author

Normalizes data in K dimensions using principal curves — normalizePrincipalCurve.matrix

<dl>

 <dt>x</dt>
<dd>An NxK <code><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></code> where the columns represent the
 (K &gt;= 2) dimensions.</dd>

 <dt>...</dt>
<dd>Additional arguments passed to
 <code>fitPrincipalCurve</code> used for fitting the model.</dd>

 <dt>center</dt>
<dd>If <code><a href='https://rdrr.io/r/base/logical.html'>TRUE</a></code>, normalized data is centered such that the median
 signal in each dimension is at zero.</dd>

 <dt>returnFit</dt>
<dd>If <code><a href='https://rdrr.io/r/base/logical.html'>TRUE</a></code>, the fitted principal curve parameters are
 returned as an attribute.</dd>

</dl>

normalizePrincipalCurve.matrix: Normalizes data in K dimensions using principal curves

Description

Usage

Value

Arguments

Author

References

See Also