---
title: "Case Study: Genomic Data Analysis with missoNet"
author: "Yixiao Zeng, Celia M. T. Greenwood"
date: "`r Sys.Date()`"
output: 
  rmarkdown::html_vignette:
    toc: true
    toc_depth: 3
    number_sections: true
    fig_width: 8
    fig_height: 6
vignette: >
  %\VignetteIndexEntry{Case Study: Genomic Data Analysis with missoNet}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.width = 8,
  fig.height = 6,
  fig.align = "center",
  out.width = "95%",
  dpi = 90,
  message = FALSE,
  warning = FALSE
)
options(width = 100)
```

# Introduction

This case study demonstrates a complete analysis pipeline using **missoNet** for genomic data analysis, specifically for regional DNA methylation QTL (meQTL) mapping. We'll analyze how genetic variants (SNPs) influence DNA methylation levels across multiple CpG sites while accounting for missing data and network structure among CpG sites.

## Scientific Context

In epigenome-wide association studies (EWAS):

* ***Predictors***: Single nucleotide polymorphisms (SNPs)
* ***Responses***: DNA methylation levels at CpG sites
* ***Challenge***: Missing methylation measurements due to technical issues
* ***Goal***: Identify genetic regulation of methylation and CpG co-regulation patterns

# Data Generation and Preparation

```{r}
# Load required packages
library(missoNet)
library(ggplot2)
library(reshape2)
library(gridExtra)

# Set ggplot theme
theme_set(theme_minimal(base_size = 11))
```

## Simulating Realistic Genomic Data

```{r}
# Set dimensions mimicking a genomic region
n <- 500   # Number of samples
p <- 80   # Number of SNPs in the region
q <- 20    # Number of CpG sites

# Create realistic correlation structure
# SNPs: Linkage disequilibrium (LD) blocks
create_ld_structure <- function(p, n_blocks = 5, within_block_cor = 0.8) {
  Sigma <- matrix(0, p, p)
  block_size <- p / n_blocks
  
  for (b in 1:n_blocks) {
    idx <- ((b-1)*block_size + 1):(b*block_size)
    for (i in idx) {
      for (j in idx) {
        Sigma[i, j] <- within_block_cor^abs(i - j)
      }
    }
  }
  diag(Sigma) <- 1
  return(Sigma)
}

Sigma.X <- create_ld_structure(p, n_blocks = 5)

# Variable missing rates (technical dropout patterns)
# Higher missingness for CpG sites with extreme GC content
gc_content <- runif(q, 0.3, 0.7)  # Simulated GC content
rho_vec <- 0.05 + 0.4 * (abs(gc_content - 0.5) / 0.2)^2  # U-shaped missing pattern

# Generate the data
sim <- generateData(
  n = n,
  p = p, 
  q = q,
  rho = rho_vec,
  missing.type = "MAR",  # Missing depends on technical factors
  Sigma.X = Sigma.X,
  Beta.row.sparsity = 0.15,  # 15% of SNPs are meQTLs
  Beta.elm.sparsity = 0.4,     # Each meQTL affects 40% of CpGs
  seed = 666
)

# Add meaningful variable names
colnames(sim$X) <- sprintf("rs%d", 1000000 + 1:p)  # SNP IDs
colnames(sim$Y) <- sprintf("cg%d", 2000000 + 1:q)  # CpG IDs
colnames(sim$Z) <- colnames(sim$Y)
rownames(sim$X) <- rownames(sim$Y) <- rownames(sim$Z) <- paste0("Sample", 1:n)

{
  cat("\nDataset Summary:\n")
  cat("================\n")
  cat("Samples:", n, "\n")
  cat("SNPs:", p, "\n")
  cat("CpG sites:", q, "\n")
  cat("Overall missing rate:", sprintf("%.1f%%", mean(is.na(sim$Z)) * 100), "\n")
  cat("True meQTLs:", sum(rowSums(abs(sim$Beta)) > 0), "\n")
}
```

# Exploratory Data Analysis

## Missing Data Patterns

```{r}
# Analyze missing patterns
miss_by_cpg <- colMeans(is.na(sim$Z))
miss_by_sample <- rowMeans(is.na(sim$Z))

# Create visualization
par(mfrow = c(2, 2))

# 1. Missing rate by CpG
plot(miss_by_cpg, type = "h", lwd = 2, col = "steelblue",
     xlab = "CpG Site", ylab = "Missing Rate",
     main = "Missing Data by CpG Site")
abline(h = mean(miss_by_cpg), col = "red", lty = 2)

# 2. Missing rate by sample
hist(miss_by_sample, breaks = 20, col = "lightblue",
     xlab = "Missing Rate", main = "Distribution of Missing Rates (Samples)")
abline(v = mean(miss_by_sample), col = "red", lwd = 2)

# 3. Heatmap of missingness
image(t(is.na(sim$Z[1:100, ])), col = c("white", "darkred"),
      xlab = "CpG Site", ylab = "Sample (first 100)",
      main = "Missing Data Pattern")

# 4. Correlation of missingness with GC content
plot(gc_content, miss_by_cpg, pch = 19, col = "darkblue",
     xlab = "GC Content", ylab = "Missing Rate",
     main = "Technical Dropout vs GC Content")
lines(lowess(gc_content, miss_by_cpg), col = "red", lwd = 2)
```

# Methylation Correlation Structure

```{r}
# Use complete data for visualization
Y_complete <- sim$Y
cor_cpg <- cor(Y_complete)

# Create enhanced heatmap
library(RColorBrewer)
colors <- colorRampPalette(brewer.pal(9, "RdBu"))(100)

heatmap(cor_cpg, 
        col = rev(colors),
        symm = TRUE,
        main = "CpG Methylation Correlation Structure",
        xlab = "CpG Sites", ylab = "CpG Sites",
        margins = c(8, 8))

# Identify CpG modules
hc <- hclust(as.dist(1 - abs(cor_cpg)))
modules <- cutree(hc, k = 3)
cat("\nCpG modules identified:", table(modules), "\n")
```

# Model Fitting

## Initial Parameter Selection

```{r}
fit_initial <- missoNet(
  X = sim$X,
  Y = sim$Z,
  n.lambda.beta = 15,
  n.lambda.theta = 15,
  GoF = "BIC",
  adaptive.search = TRUE,  # Fast exploration
  verbose = 1
)

# Examine initial selection
{
  cat("\nStep 1: Initial parameter exploration\n")
  cat("=====================================\n")
  cat("  Lambda.beta:", fit_initial$est.min$lambda.beta, "\n")
  cat("  Lambda.theta:", fit_initial$est.min$lambda.theta, "\n")
  cat("  Active SNPs:", sum(rowSums(abs(fit_initial$est.min$Beta)) > 1e-8), "\n")
  cat("  Network edges:", 
      sum(abs(fit_initial$est.min$Theta[upper.tri(fit_initial$est.min$Theta)]) > 1e-8), "\n")
}
```
## Cross-Validation

```{r}
# Define refined grid based on initial exploration
lambda.beta.refined <- 10^(seq(
  log10(min(1, fit_initial$est.min$lambda.beta * 20)),
  log10(max(0.005, fit_initial$est.min$lambda.beta / 20)),
  length.out = 25
))

lambda.theta.refined <- 10^(seq(
  log10(min(1, fit_initial$est.min$lambda.theta * 20)),
  log10(max(0.005, fit_initial$est.min$lambda.theta / 20)),
  length.out = 25
))

# Perform 10-fold cross-validation
cvfit <- cv.missoNet(
  X = sim$X,
  Y = sim$Z,
  kfold = 5,
  lambda.beta = lambda.beta.refined,
  lambda.theta = lambda.theta.refined,
  compute.1se = TRUE,
  verbose = 0,
  seed = 123
)
```

## Model Comparison

```{r}
# Compare different model choices
models <- list(
  "CV Minimum" = cvfit$est.min,
  "1SE Beta" = cvfit$est.1se.beta,
  "1SE Theta" = cvfit$est.1se.theta,
  "Initial BIC" = fit_initial$est.min
)

comparison <- data.frame(
  Model = names(models),
  Lambda.Beta = sapply(models, function(x) x$lambda.beta),
  Lambda.Theta = sapply(models, function(x) x$lambda.theta),
  Active.SNPs = sapply(models, function(x) 
    sum(rowSums(abs(x$Beta)) > 1e-8)),
  Total.Effects = sapply(models, function(x)
    sum(abs(x$Beta) > 1e-8)),
  Network.Edges = sapply(models, function(x)
    sum(abs(x$Theta[upper.tri(x$Theta)]) > 1e-8))
)

print(comparison, digits = 4)

# Select final model
final_model <- cvfit$est.1se.beta
```

# Results Interpretation

## Identified meQTLs

```{r}
# Extract coefficients
Beta <- final_model$Beta
rownames(Beta) <- colnames(sim$X)
colnames(Beta) <- colnames(sim$Z)

# Identify significant associations
threshold <- 1e-3
sig_meqtls <- which(abs(Beta) > threshold, arr.ind = TRUE)

if (nrow(sig_meqtls) > 0) {
  meqtl_df <- data.frame(
    SNP = rownames(Beta)[sig_meqtls[,1]],
    CpG = colnames(Beta)[sig_meqtls[,2]],
    Effect = Beta[sig_meqtls],
    AbsEffect = abs(Beta[sig_meqtls])
  )
  meqtl_df <- meqtl_df[order(meqtl_df$AbsEffect, decreasing = TRUE), ]
  
  cat("Top 15 meQTL associations:\n")
  print(head(meqtl_df, 15), digits = 3)
  
  # Visualization
  top_snps <- unique(meqtl_df$SNP[1:min(30, nrow(meqtl_df))])
  Beta_subset <- Beta[top_snps, , drop = FALSE]
  
  # Create heatmap
  par(mfrow = c(1, 1))
  colors <- colorRampPalette(c("blue", "white", "red"))(100)
  heatmap(as.matrix(Beta_subset), 
          col = colors,
          scale = "none",
          main = "Top meQTL Effects",
          xlab = "CpG Sites", 
          ylab = "SNPs",
          margins = c(8, 8))
}
```

# CpG Network Analysis

```{r}
# Extract precision matrix and convert to partial correlations
Theta <- final_model$Theta
rownames(Theta) <- colnames(Theta) <- colnames(sim$Z)

# Compute partial correlations
partial_cor <- -cov2cor(Theta)
diag(partial_cor) <- 0

# Network statistics
edge_threshold <- 0.1
n_edges <- sum(abs(partial_cor[upper.tri(partial_cor)]) > edge_threshold)
{
  cat("\nNetwork Statistics:\n")
  cat("  Total possible edges:", q * (q-1) / 2, "\n")
  cat("  Selected edges (|r| >", edge_threshold, "):", n_edges, "\n")
  cat("  Network density:", sprintf("%.1f%%", 100 * n_edges / (q * (q-1) / 2)), "\n")
}

# Identify hub CpGs
degree <- colSums(abs(partial_cor) > edge_threshold)
hub_cpgs <- names(sort(degree, decreasing = TRUE)[1:5])
cat("\nHub CpG sites (highest connectivity):\n")
for (cpg in hub_cpgs) {
  cat("  ", cpg, ": degree =", degree[cpg], "\n")
}

# Visualize network
if (requireNamespace("igraph", quietly = TRUE)) {
  library(igraph)
  
  # Create network from significant edges
  edges <- which(abs(partial_cor) > 0.15 & upper.tri(partial_cor), arr.ind = TRUE)
  if (nrow(edges) > 0) {
    edge_list <- data.frame(
      from = rownames(partial_cor)[edges[,1]],
      to = colnames(partial_cor)[edges[,2]],
      weight = abs(partial_cor[edges])
    )
    
    g <- graph_from_data_frame(edge_list, directed = FALSE)
    
    # Node properties
    V(g)$size <- 5 + sqrt(degree[V(g)$name]) * 3
    V(g)$color <- ifelse(V(g)$name %in% hub_cpgs, "red", "lightblue")
    
    # Plot
    par(mfrow = c(1, 1))
    plot(g, 
         layout = layout_with_fr(g),
         vertex.label.cex = 0.7,
         edge.width = E(g)$weight * 3,
         main = "CpG Conditional Dependency Network")
    legend("topright", legend = c("Hub CpG", "Regular CpG"),
           pch = 21, pt.bg = c("red", "lightblue"), pt.cex = 2)
  }
}
```

# SNP-CpG-Network Integration

```{r}
# Analyze how meQTLs relate to network structure
active_snps <- which(rowSums(abs(Beta)) > threshold)

if (length(active_snps) > 0) {
  cat("\nIntegration Analysis:\n")
  cat("=====================\n")
  # For each active SNP, check which CpGs it affects
  for (i in active_snps[1:min(5, length(active_snps))]) {
    affected_cpgs <- which(abs(Beta[i,]) > threshold)
    if (length(affected_cpgs) > 1) {
      # Check if affected CpGs are connected in the network
      subnet_partial <- partial_cor[affected_cpgs, affected_cpgs]
      mean_connection <- mean(abs(subnet_partial[upper.tri(subnet_partial)]))
      
      cat("\n", rownames(Beta)[i], "affects", length(affected_cpgs), "CpGs\n")
      cat("Mean network connection among affected CpGs:", 
          round(mean_connection, 3), "\n")
      cat("Affected CpGs:", paste(colnames(Beta)[affected_cpgs], collapse = ", "), "\n")
    }
  }
}
```

# Model Validation

## Prediction Performance

```{r}
# Split data for validation
n_train <- round(0.75 * n)
train_idx <- sample(n, n_train)
test_idx <- setdiff(1:n, train_idx)

# Refit on training data
cvfit_train <- cv.missoNet(
  X = sim$X[train_idx, ],
  Y = sim$Z[train_idx, ],
  kfold = 5,
  lambda.beta = lambda.beta.refined,
  lambda.theta = lambda.theta.refined,
  verbose = 0
)

# Predictions
Y_pred <- predict(cvfit_train, newx = sim$X[test_idx, ])
Y_test <- sim$Y[test_idx, ]  # True complete values

# Calculate performance metrics
mse_per_cpg <- colMeans((Y_pred - Y_test)^2)
cor_per_cpg <- sapply(1:q, function(j) cor(Y_pred[,j], Y_test[,j]))

# Visualization
par(mfrow = c(1, 2))

# MSE vs missing rate
plot(miss_by_cpg, mse_per_cpg, pch = 19, col = "darkblue",
     xlab = "Missing Rate", ylab = "Prediction MSE",
     main = "Prediction Error vs Missing Rate")
lines(lowess(miss_by_cpg, mse_per_cpg), col = "red", lwd = 2)

# Correlation vs missing rate
plot(miss_by_cpg, cor_per_cpg, pch = 19, col = "darkgreen",
     xlab = "Missing Rate", ylab = "Prediction Correlation",
     main = "Prediction Accuracy vs Missing Rate")
lines(lowess(miss_by_cpg, cor_per_cpg), col = "red", lwd = 2)

{
  cat("\nPrediction Performance:\n")
  cat("  Mean MSE:", round(mean(mse_per_cpg), 4), "\n")
  cat("  Mean correlation:", round(mean(cor_per_cpg), 3), "\n")
  cat("  Worst CpG MSE:", round(max(mse_per_cpg), 4), "\n")
  cat("  Best CpG correlation:", round(max(cor_per_cpg), 3), "\n")
}
```

## Stability Assessment

```{r}
# Bootstrap stability (simplified for demonstration)
n_boot <- 10
selection_freq_beta <- matrix(0, p, q)
selection_freq_theta <- matrix(0, q, q)

for (b in 1:n_boot) {
  # Bootstrap sample
  boot_idx <- sample(n, replace = TRUE)
  
  # Fit model
  fit_boot <- missoNet(
    X = sim$X[boot_idx, ],
    Y = sim$Z[boot_idx, ],
    lambda.beta = final_model$lambda.beta,
    lambda.theta = final_model$lambda.theta,
    verbose = 0
  )
  
  # Track selections
  selection_freq_beta <- selection_freq_beta + (abs(fit_boot$est.min$Beta) > threshold)
  selection_freq_theta <- selection_freq_theta + 
    (abs(fit_boot$est.min$Theta) > edge_threshold)
}

# Normalize
selection_freq_beta <- selection_freq_beta / n_boot
selection_freq_theta <- selection_freq_theta / n_boot

# Identify stable features
stable_meqtls <- which(selection_freq_beta > 0.8, arr.ind = TRUE)
stable_edges <- which(selection_freq_theta > 0.8 & upper.tri(selection_freq_theta), 
                     arr.ind = TRUE)

{
  cat("\nStability Results:\n")
  cat("  Stable meQTLs (>80% selection):", nrow(stable_meqtls), "\n")
  cat("  Stable network edges (>80% selection):", nrow(stable_edges), "\n")
}

if (nrow(stable_meqtls) > 0) {
  cat("\nMost stable meQTL associations:\n")
  stable_df <- data.frame(
    SNP = colnames(sim$X)[stable_meqtls[,1]],
    CpG = colnames(sim$Z)[stable_meqtls[,2]],
    Frequency = selection_freq_beta[stable_meqtls]
  )
  print(head(stable_df[order(stable_df$Frequency, decreasing = TRUE), ], 10))
}
```

# Biological Interpretation

## Gene Set Enrichment Analysis (Simulated)

```{r}
# Annotate SNPs with genes (simulated)
active_snp_ids <- which(rowSums(abs(Beta)) > threshold)
if (length(active_snp_ids) > 0) {
  gene_names <- paste0("GENE", sample(1:50, length(active_snp_ids), replace = TRUE))
  
  snp_annotation <- data.frame(
    SNP = colnames(sim$X)[active_snp_ids],
    Gene = gene_names,
    Effect_Size = rowSums(abs(Beta[active_snp_ids, ]))
  )
  
  cat("Genes with meQTLs:\n")
  gene_summary <- aggregate(Effect_Size ~ Gene, snp_annotation, sum)
  gene_summary <- gene_summary[order(gene_summary$Effect_Size, decreasing = TRUE), ]
  print(head(gene_summary, 10))
}

# CpG annotation (simulated)
cpg_annotation <- data.frame(
  CpG = colnames(sim$Z),
  Region = sample(c("Promoter", "Gene Body", "Enhancer", "Intergenic"), 
                  q, replace = TRUE, prob = c(0.4, 0.3, 0.2, 0.1)),
  Island = sample(c("Island", "Shore", "Shelf", "Open Sea"),
                  q, replace = TRUE, prob = c(0.3, 0.2, 0.2, 0.3))
)

{
  cat("\nCpG distribution by genomic region:\n")
  print(table(cpg_annotation$Region))
}

{
  cat("\nCpG distribution by island status:\n")
  print(table(cpg_annotation$Island))
}
```

# Reporting and Export

## Summary Report

```{r, echo = FALSE, include = TRUE}
cat("\n========================================\n")
cat("       ANALYSIS SUMMARY REPORT\n")
cat("========================================\n\n")

cat("\nDATA CHARACTERISTICS:\n")
cat("--------------------\n")
cat("• Samples analyzed:", n, "\n")
cat("• SNPs tested:", p, "\n")
cat("• CpG sites measured:", q, "\n")
cat("• Missing data rate:", sprintf("%.1f%%", mean(is.na(sim$Z)) * 100), "\n")
cat("• Missing pattern: MAR (technical dropout)\n\n")

cat("\nMODEL SELECTION:\n")
cat("---------------\n")
cat("• Method: 5-fold cross-validation\n")
cat("• Selection criterion: 1-SE.Beta CV error\n")
cat("• Lambda (Beta):", sprintf("%.4f", final_model$lambda.beta), "\n")
cat("• Lambda (Theta):", sprintf("%.4f", final_model$lambda.theta), "\n\n")

cat("\nKEY FINDINGS:\n")
cat("------------\n")
cat("• meQTLs identified:", sum(rowSums(abs(Beta)) > threshold), "/", p, "SNPs\n")
cat("• SNP-CpG associations:", sum(abs(Beta) > threshold), "\n")
cat("• CpG network edges:", n_edges, "/", q*(q-1)/2, "possible\n")
cat("• Hub CpGs identified:", length(hub_cpgs), "\n\n")

cat("\nMODEL PERFORMANCE:\n")
cat("-----------------\n")
cat("• Mean prediction correlation:", sprintf("%.3f", mean(cor_per_cpg)), "\n")
cat("• Mean prediction MSE:", sprintf("%.4f", mean(mse_per_cpg)), "\n")
cat("• Stability (bootstrap):", sprintf("%.0f%%", 
    100 * nrow(stable_meqtls) / max(sum(abs(Beta) > threshold), 1)), 
    "of associations stable\n\n")

cat("\nBIOLOGICAL INSIGHTS (SIMULATED):\n")
cat("-------------------\n")
cat("• Primary affected regions: Promoters and gene bodies\n")
cat("• Network structure suggests co-regulated CpG modules\n")
cat("• Hub CpGs may represent key regulatory sites\n")
```

# Conclusions

This case study demonstrated a complete genomic data analysis workflow using **missoNet**:

* ***Data Preparation***: Handled realistic missing patterns and correlation structures
* ***Model Selection***: Used two-stage approach with cross-validation
* ***meQTL Discovery***: Identified genetic variants affecting methylation
* ***Network Analysis***: Revealed co-regulation patterns among CpG sites
* ***Validation***: Assessed prediction accuracy and selection stability
* ***Integration***: Connected genetic effects with epigenetic networks

The **missoNet** framework successfully:

* Handled 10-30% missing data without imputation
* Identified sparse genetic effects in high-dimensional setting
* Revealed network structure among responses
* Provided stable, interpretable results

