LorMe-class

A container class for microbial ecology data integration, including metadata,
feature tables, configuration parameters, and phylogenetic tree.

Provides a robust collection of functions tailored for microbial ecology analysis, encompassing both data analysis and visualization. It introduces an encapsulation feature that streamlines the process into a summary object. With the initial configuration of this summary object, users can execute a wide range of analyses with a single line of code, requiring only two essential parameters for setup. The package delivers comprehensive outputs including analysis objects, statistical outcomes, and visualization-ready data, enhancing the efficiency of research workflows. Designed with user-friendliness in mind, it caters to both novices and seasoned researchers, offering an intuitive interface coupled with adaptable customization options to meet diverse analytical needs.

Ningqi Wang

LorMe

Lightweight One-Line Resolving Microbial Ecology Program

Yaozhong Zhang

Gaofei Jiang

LorMe-class function

<dl>
<dt><code>groupfile</code></dt>
<dd>data.frame: Sample metadata</dd></dl>
<dt><code>data</code></dt>
<dd>list: Named list containing feature and taxonomy tables</dd>
<dt><code>configuration</code></dt>
<dd>list: Analysis configuration parameters</dd>
<dt><code>tree</code></dt>
<dd>phyloOrNULL: Phylogenetic tree (NULL if not provided, requires ape package)</dd>

Slots

<dl>
<dt><code>show(object)</code></dt>
<dd>Print summary of the LorMe object</dd></dl><dt><code>x$name</code></dt>
<dd>Access slots or data elements via $</dd><dt><code>.DollarNames(x, pattern)</code></dt>
<dd>Tab completion for $ access</dd>

Methods

LorMe S4 class — LorMe-class

<dl>
<dt><code>groupfile</code></dt>
<dd>data.frame: Sample metadata</dd>


<dt><code>data</code></dt>
<dd>list: Named list containing feature and taxonomy tables</dd>


<dt><code>configuration</code></dt>
<dd>list: Analysis configuration parameters</dd>


<dt><code>tree</code></dt>
<dd>phyloOrNULL: Phylogenetic tree (NULL if not provided, requires ape package)</dd>


</dl>

<dl>
<dt><code>show(object)</code></dt>
<dd>Print summary of the LorMe object</dd>

<dt><code>x$name</code></dt>
<dd>Access slots or data elements via $</dd>

<dt><code>.DollarNames(x, pattern)</code></dt>
<dd>Tab completion for $ access</dd>


</dl>

LorMe-class: LorMe S4 class

Description

Arguments

Slots

Methods