ko_to_kegg_reference: KO to KEGG Pathway Reference Data

In ggpicrust2: Make 'PICRUSt2' Output Analysis and Visualization Easier

KO to KEGG Pathway Reference Data

Description

A comprehensive mapping between KEGG Orthology (KO) identifiers and KEGG pathways. This dataset contains mappings covering 532 pathways and 23,466 unique KO IDs, filtered to include only real KEGG pathway maps (5-digit IDs).

Usage

ko_to_kegg_reference

Format

A data frame with 9 variables:

pathway_id

KEGG pathway identifier (e.g., "ko00010")

pathway_number

KEGG pathway number

pathway_name

Full name of the pathway

ko_id

KEGG Orthology identifier (e.g., "K00001")

ko_description

Description of the KO

ec_number

EC number associated with the KO (if applicable)

level1

KEGG pathway hierarchy Level 1 classification

level2

KEGG pathway hierarchy Level 2 classification

level3

KEGG pathway hierarchy Level 3 classification

Details

This reference data is used by the ko2kegg_abundance function to convert KO abundance data to KEGG pathway abundance. The data is stored internally and does not require internet connectivity to use.

The dataset covers major KEGG pathway categories including:

• Metabolism

• Genetic Information Processing

• Environmental Information Processing

• Cellular Processes

• Organismal Systems

• Human Diseases

Source

KEGG database (https://www.kegg.jp/)

See Also

ko2kegg_abundance for converting KO abundance to pathway abundance

Examples

# Load the reference data
data(ko_to_kegg_reference)

# View structure
str(ko_to_kegg_reference)

# Get unique pathways
unique_pathways <- unique(ko_to_kegg_reference$pathway_id)
length(unique_pathways)

# Find KOs for a specific pathway
glycolysis_kos <- ko_to_kegg_reference[ko_to_kegg_reference$pathway_id == "ko00010", ]
head(glycolysis_kos)

ggpicrust2 documentation built on April 10, 2026, 5:06 p.m.