estimateComponents

Estimates the values of \(r\) and \(\sigma\) in a model \(X \sim N(0, \sigma^2
(r Q + (1 - r)I))\).

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

estimateComponents function

<dl><dt>X</dt>
<dd>An \(n \times p\) data matrix.</dd>
<dt>Q</dt>
<dd>A \(p \times p\) matrix giving the prior variance on the
rows of <code>X</code>.</dd>
<dt>Qeig</dt>
<dd>If the eigendecomposition of <code>Q</code> is already computed, it
can be included here.</dd></dl>

Arguments

Estimate parameters in hierarchical model — estimateComponents

<dl>

<dt>X</dt>
<dd>An \(n \times p\) data matrix.</dd>


<dt>Q</dt>
<dd>A \(p \times p\) matrix giving the prior variance on the
rows of <code>X</code>.</dd>


<dt>Qeig</dt>
<dd>If the eigendecomposition of <code>Q</code> is already computed, it
can be included here.</dd>

</dl>

estimateComponents: Estimate parameters in hierarchical model

Description

Usage

Value

Arguments

Examples