process_step_comma

Handles comma-separated KOs by applying the specified scaling method (sum or max).
Processes multiple KOs separated by commas and aggregates them into a single row.

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_comma 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 comma-separated KO IDs (default: "K14126,K14127,K14128")</dd>
<dt>aggregrate_rowname</dt>
<dd>Base name for row aggregation (default: 'step_1')</dd>
<dt>step_count</dt>
<dd>Processing step counter (default: 1)</dd>
<dt>comma_scale_method</dt>
<dd>Scaling method for comma-separated KOs ("sum" or "max")</dd></dl>

Arguments

Process Comma-Separated KOs with Specified Scaling Method — process_step_comma

<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 comma-separated KO IDs (default: "K14126,K14127,K14128")</dd>


<dt>aggregrate_rowname</dt>
<dd>Base name for row aggregation (default: 'step_1')</dd>


<dt>step_count</dt>
<dd>Processing step counter (default: 1)</dd>


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

</dl>

process_step_comma: Process Comma-Separated KOs with Specified Scaling Method

Description

Usage

Value

Arguments