gpca

Performs standard gPCA with <code>k</code> components on a data matrix <code>X</code> with
row inner product <code>Q</code> and weights <code>D</code>.

Implements adaptive gPCA, as described in: Fukuyama, J. (2017)
<arXiv:1702.00501>. The package also includes functionality for applying
the method to 'phyloseq' objects so that the method can be easily applied
to microbiome data and a 'shiny' app for interactive visualization.

Julia Fukuyama

adaptiveGPCA

Adaptive Generalized PCA

gpca function

<dl><dt>X</dt>
<dd>A data matrix of size \(n \times p\).</dd>
<dt>Q</dt>
<dd>An inner product matrix for the rows, either as a \(p
\times p\) matrix or an eigendecomposition of such a matrix.</dd>
<dt>D</dt>
<dd>Sample weights, a vector of length \(n\).</dd>
<dt>k</dt>
<dd>The number of components to return.</dd></dl>

Arguments

gPCA — gpca

<dl>

<dt>X</dt>
<dd>A data matrix of size \(n \times p\).</dd>


<dt>Q</dt>
<dd>An inner product matrix for the rows, either as a \(p
\times p\) matrix or an eigendecomposition of such a matrix.</dd>


<dt>D</dt>
<dd>Sample weights, a vector of length \(n\).</dd>


<dt>k</dt>
<dd>The number of components to return.</dd>

</dl>

gpca: gPCA

Description

Usage

Value

Arguments

Examples