process_module_structure

Filters and merges pathway information with sample KO data for a specific module.
Returns a merged dataframe containing KO abundance data and pathway definitions.

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_module_structure function

<dl><dt>pathway_infor</dt>
<dd>Data frame containing pathway information, see examples.</dd>
<dt>Sample_KO</dt>
<dd>Dataframe containing KO abundance data with KO IDs as row names</dd>
<dt>module</dt>
<dd>Character string of the module ID to process (e.g. "M00563")</dd></dl>

Arguments

Process Module Structure Data — process_module_structure

<dl>

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


<dt>Sample_KO</dt>
<dd>Dataframe containing KO abundance data with KO IDs as row names</dd>


<dt>module</dt>
<dd>Character string of the module ID to process (e.g. "M00563")</dd>

</dl>

process_module_structure: Process Module Structure Data

Description

Usage

Value

Arguments