KO_Sample_wide

A test dataset (wide-format) showing the relative abundance of KEGG Orthology (KO) entries
across multiple microbial samples. Values represent normalized abundance metrics
(e.g., TPM, RPKM, relative percentage, presence/absence).

datasets

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

KO_Sample_wide function

A data frame with 2495 rows (KO entries) and 5 variables:<dl>
<dt>KO</dt>
<dd>Character. KEGG Orthology ID (e.g., "K00001").</dd><dt>Marinobacter salarius</dt>
<dd>Numeric. Abundance in Genome "Marinobacter salarius".</dd><dt>Pseudooceanicola nanhaiensis</dt>
<dd>Numeric. Abundance in Genome "Pseudooceanicola nanhaiensis".</dd><dt>Alteromonas australica</dt>
<dd>Numeric. Abundance in Genome "Alteromonas australica".</dd><dt>Henriciella pelagia</dt>
<dd>Numeric. Abundance in Genome "Henriciella pelagia".</dd>
</dl>

Format

KEGG Orthology (KO) Abundance/Presence Across Microbial Samples or Genomes — KO_Sample_wide

A data frame with 2495 rows (KO entries) and 5 variables:<dl>
<dt>KO</dt>
<dd>Character. KEGG Orthology ID (e.g., "K00001").</dd>

<dt>Marinobacter salarius</dt>
<dd>Numeric. Abundance in Genome "Marinobacter salarius".</dd>

<dt>Pseudooceanicola nanhaiensis</dt>
<dd>Numeric. Abundance in Genome "Pseudooceanicola nanhaiensis".</dd>

<dt>Alteromonas australica</dt>
<dd>Numeric. Abundance in Genome "Alteromonas australica".</dd>

<dt>Henriciella pelagia</dt>
<dd>Numeric. Abundance in Genome "Henriciella pelagia".</dd>


</dl>

KO_Sample_wide: KEGG Orthology (KO) Abundance/Presence Across Microbial Samples or Genomes

Description

Usage

Arguments

Format