process_step_direct

Processes KO abundances directly without any special scaling or aggregation.
Simply extracts the specified KOs from the abundance table while maintaining
the original module metadata.

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_step_direct function

<dl><dt>module_abundance</dt>
<dd>Data frame containing KO abundance data with required columns:
Orthology_Entry, Module_Entry, Definition</dd>
<dt>KOs</dt>
<dd>Character vector of KO IDs to extract (default: c("K14126","K14128","K14127"))</dd></dl>

Arguments

Direct KO Processing Without Special Handling — process_step_direct

<dl>

<dt>module_abundance</dt>
<dd>Data frame containing KO abundance data with required columns:
Orthology_Entry, Module_Entry, Definition</dd>


<dt>KOs</dt>
<dd>Character vector of KO IDs to extract (default: c("K14126","K14128","K14127"))</dd>

</dl>

process_step_direct: Direct KO Processing Without Special Handling

Description

Usage

Value

Arguments