processPhyloseq

Takes a phyloseq object and creates the matrices necessary to do
adaptive gPCA.

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

processPhyloseq function

<dl><dt>physeq</dt>
<dd>A <code>phyloseq</code> object, from the
phyloseq package.</dd>
<dt>ca</dt>
<dd>If TRUE, do the normalization as for correspondence
analysis (transform counts to relative abundances, compute sample
weights, center the relative abundances according to the sample
weights). Otherwise, simply center the data.</dd></dl>

Arguments

Make the input matrices for adaptive gPCA — processPhyloseq

<dl>

<dt>physeq</dt>
<dd>A <code>phyloseq</code> object, from the
phyloseq package.</dd>


<dt>ca</dt>
<dd>If TRUE, do the normalization as for correspondence
analysis (transform counts to relative abundances, compute sample
weights, center the relative abundances according to the sample
weights). Otherwise, simply center the data.</dd>

</dl>

processPhyloseq: Make the input matrices for adaptive gPCA

Description

Usage

Value

Arguments

Examples