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# mclink: Metabolic Pathway Completeness and Abundance Analysis

## Overview

`mclink` provides comprehensive tools for analyzing metabolic pathway completeness and abundance using KEGG Orthology (KO) data from (meta)genomic and (meta)transcriptomic studies. Key features include:

- **Dual analysis modes**: Completeness (presence/absence) and abundance-weighted scoring
- **Flexible input**: Works with built-in KEGG references or custom datasets
- **Smart KO handling**: Specialized methods for plus-separated (subunits) and comma-separated (isoforms) KOs
- **Publication-ready outputs**: Pathway coverage metrics and detailed KO detection reports

## Installation

```r
# Install from GitHub
if (!require("devtools")) install.packages("devtools")
devtools::install_github("LiuyangLee/mclink")

Quick Start

library(mclink)

# Using built-in datasets
data(KO_pathway_ref)
data(KO_Sample_wide)

# Analyze selected pathways
selected_modules <- c("M00176", "M00165", "M00173", "M00374")
results <- mclink(
  ref = KO_pathway_ref[KO_pathway_ref$Module_Entry %in% selected_modules, ],
  data = KO_Sample_wide,
  table_feature = "completeness"
)

# Access results
head(results$coverage)      # Pathway coverage metrics
head(results$detected_KOs)  # Detected KOs per pathway

Key Features

Analysis Modes

• Completeness analysis: Binary presence/absence scoring
• Abundance analysis: Weighted by KO abundance levels

Specialized KO Handling

Output Options

• File exports: TSV format for both coverage and KO detection
• Pathway-split outputs: Optional separate files per pathway

Documentation

Full function reference:

?mclink::mclink

Citation

If you use mclink in your research, please cite:

Li, L., Huang, D., Hu, Y., Rudling, N. M., Canniffe, D. P., Wang, F., & Wang, Y. “Globally distributed Myxococcota with photosynthesis gene clusters illuminate the origin and evolution of a potentially chimeric lifestyle.” Nature Communications (2023), 14, 6450. https://doi.org/10.1038/s41467-023-42193-7

Dependencies

• R (≥ 3.5)
• data.table (≥ 1.17.0)
• dplyr (≥ 1.1.4)
• stringr (≥ 1.5.1)
• tibble (≥ 3.2.1)

License

GPL-3 © Liuyang Li

Contact

• Maintainer: Liuyang Li cyanobacteria@yeah.net
• Bug reports: https://github.com/LiuyangLee/mclink/issues ```

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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