merge_module_name

Merges pathway information with a module table to create a sample-by-module matrix
with proper module names. Ensures all modules are represented in the output.

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

merge_module_name function

<dl><dt>pathway_infor</dt>
<dd>Data frame containing pathway information, see examples.</dd>
<dt>module_table</dt>
<dd>Data frame containing module data with:
- Module_Entry: Matching module identifiers
- Orthology_Entry: KO identifiers
- Definition: Module definitions
- Sample columns with abundance values</dd></dl>

Arguments

Merge Module Information with Module Table — merge_module_name

<dl>

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


<dt>module_table</dt>
<dd>Data frame containing module data with:
- Module_Entry: Matching module identifiers
- Orthology_Entry: KO identifiers
- Definition: Module definitions
- Sample columns with abundance values</dd>

</dl>

merge_module_name: Merge Module Information with Module Table

Description

Usage

Value

Arguments