process_step_plus

Handles plus-separated KOs by applying the specified scaling method (mean, min, or max).
Processes multiple KOs separated by plus signs and aggregates them into a single row.
Note: For mean calculation, uses the sum of existing KO abundances divided by total
number of KOs (including those with zero abundance in all samples).

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_plus 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 string of plus-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>plus_scale_method</dt>
<dd>Scaling method for plus-separated KOs ("mean", "min", or "max")</dd></dl>

Arguments

Process Plus-Separated KOs with Specified Scaling Method — process_step_plus

<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 string of plus-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>plus_scale_method</dt>
<dd>Scaling method for plus-separated KOs ("mean", "min", or "max")</dd>

</dl>

process_step_plus: Process Plus-Separated KOs with Specified Scaling Method

Description

Usage

Value

Arguments