process_all_modules

Processes all metabolic modules in pathway information, handling each module's structure,
definition, and bracket components. Aggregates results across all modules.

Provides tools for analyzing metabolic pathway completeness, abundance, and transcripts
using KEGG Orthology (KO) data from (meta)genomic and (meta)transcriptomic studies.
Supports both completeness (presence/absence) and abundance-weighted analyses.
Includes built-in KEGG reference datasets. For more details see Li et al. (2023) <doi:10.1038/s41467-023-42193-7>.

Liuyang Li

mclink

Metabolic Pathway Completeness and Abundance Calculation

process_all_modules function

<dl><dt>pathway_infor</dt>
<dd>Data frame containing pathway information, see examples.</dd>
<dt>Sample_KO</dt>
<dd>Data frame containing KO (KEGG Orthology) sample data</dd>
<dt>plus_scale_method</dt>
<dd>Scaling method for plus-separated KOs ("mean", "min", or "max")</dd>
<dt>comma_scale_method</dt>
<dd>Scaling method for comma-separated KOs ("sum" or "max")</dd>
<dt>verbose</dt>
<dd>Logical controlling console output:<ul>
<li><code>TRUE</code> (default): Print progress messages</li>
<li><code>FALSE</code>: Silent mode</li>
</ul></dd></dl>

Arguments

Process All Modules in Pathway Information — process_all_modules

<dl>

<dt>pathway_infor</dt>
<dd>Data frame containing pathway information, see examples.</dd>


<dt>Sample_KO</dt>
<dd>Data frame containing KO (KEGG Orthology) sample data</dd>


<dt>plus_scale_method</dt>
<dd>Scaling method for plus-separated KOs ("mean", "min", or "max")</dd>


<dt>comma_scale_method</dt>
<dd>Scaling method for comma-separated KOs ("sum" or "max")</dd>


<dt>verbose</dt>
<dd>Logical controlling console output:<ul>
<li><code>TRUE</code> (default): Print progress messages</li>
<li><code>FALSE</code>: Silent mode</li>
</ul></dd>

</dl>

process_all_modules: Process All Modules in Pathway Information

Description

Usage

Value

Arguments