ko_to_kegg_reference: 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

Arguments

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

Examples

Run this code

# 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)