group_ko_by_module

Processes KO abundance data to group by metabolic modules, converting
presence/absence data into module-level KO lists. Handles missing KOs
and maintains sample-specific KO profiles.

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

group_ko_by_module function

<dl><dt>pathway_infor</dt>
<dd>Data frame containing pathway information, see examples.</dd>
<dt>Sample_KO_abundance</dt>
<dd>Data frame of KO abundances with:
- Rows as KO identifiers
- Columns as samples
- Orthology_Entry column</dd></dl>

Arguments

Group KO Abundance Data by Module — group_ko_by_module

<dl>

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


<dt>Sample_KO_abundance</dt>
<dd>Data frame of KO abundances with:
- Rows as KO identifiers
- Columns as samples
- Orthology_Entry column</dd>

</dl>

group_ko_by_module: Group KO Abundance Data by Module

Description

Usage

Value

Arguments