removeOutliers

Removes outliers in matrix containing SNP signals by identifying outlier elements. The values of the
 elements that are outliers are substituted by corresponding values
 predicted values <code>Yest=W*H</code> from the current affinity (<code>W</code>)
 and copy number (<code>H</code>) estimates.

internal

A summarization method to estimate allele-specific copy number signals for Affymetrix SNP microarrays using non-negative matrix factorization (NMF).

Henrik Bengtsson

ACNE

Affymetrix SNP Probe-Summarization using Non-Negative Matrix
Factorization

Maria Ortiz

Angel Rubio

removeOutliers function

<dl> <dt>Y</dt>
<dd>An IxK <code><a href="/link/matrix?package=ACNE&version=0.9.1" data-mini-rdoc="ACNE::matrix">matrix</a></code>.</dd> <dt>W</dt>
<dd>A Kx2 <code><a href="/link/matrix?package=ACNE&version=0.9.1" data-mini-rdoc="ACNE::matrix">matrix</a></code> of probe-affinity estimates.</dd> <dt>H</dt>
<dd>A 2xI <code><a href="/link/matrix?package=ACNE&version=0.9.1" data-mini-rdoc="ACNE::matrix">matrix</a></code> of allele-specific copy-number estimates.</dd> <dt>tau</dt>
<dd>A scalar specifying the threshold for identifying outliers.</dd> <dt>...</dt>
<dd>Not used.</dd></dl>

Arguments

Removes outliers in matrix containing SNP signals — removeOutliers

<dl>

 <dt>Y</dt>
<dd>An IxK <code><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></code>.</dd>

 <dt>W</dt>
<dd>A Kx2 <code><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></code> of probe-affinity estimates.</dd>

 <dt>H</dt>
<dd>A 2xI <code><a href='https://rdrr.io/r/base/matrix.html'>matrix</a></code> of allele-specific copy-number estimates.</dd>

 <dt>tau</dt>
<dd>A scalar specifying the threshold for identifying outliers.</dd>

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

</dl>

removeOutliers: Removes outliers in matrix containing SNP signals

Description

Usage

Value

Arguments