create_sub_module_sample

Processes pathway information and module sample data to create and export
individual pathway-specific files containing scaled module data.

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

create_sub_module_sample function

<dl><dt>pathway_infor</dt>
<dd>Data frame containing pathway information, see examples.</dd>
<dt>Module_Sample_scale</dt>
<dd>Data frame containing scaled module sample data with
module names as row names</dd>
<dt>out_DIR_Module_Sample_by_pathway</dt>
<dd>Character string specifying output directory</dd>
<dt>plus_scale_method</dt>
<dd>Scaling method for plus-separated KOs ("mean", "min", or "max")</dd>
<dt>comma_scale_method</dt>
<dd>Scaling method for comma-separated KOs ("sum" or "max")</dd></dl>

Arguments

Create and Export Pathway-Specific Module Sample Files — create_sub_module_sample

<dl>

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


<dt>Module_Sample_scale</dt>
<dd>Data frame containing scaled module sample data with
module names as row names</dd>


<dt>out_DIR_Module_Sample_by_pathway</dt>
<dd>Character string specifying output directory</dd>


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


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

</dl>

create_sub_module_sample: Create and Export Pathway-Specific Module Sample Files

Description

Usage

Value

Arguments