# 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")

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

?mclink::mclink