process_step_space

Handles space-separated KOs by calculating the mean abundance across all specified KOs.
Processes multiple KOs separated by spaces and aggregates them into a single row.
Note: For mean calculation, uses the sum of 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_space 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 space-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></dl>

Arguments

Process Space-Separated KOs with Mean Calculation — process_step_space

<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 space-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>

</dl>

process_step_space: Process Space-Separated KOs with Mean Calculation

Description

Usage

Value

Arguments