Differential Expression Analysis - Filtering and Visualization-NEWUMAP

1. Load Libraries

2. Load Data

2.1 Load CSV Files with Mean Expression

3. Summarize Results

3.1 Summary Function

summarize_markers <- function(markers) {
  num_pval0 <- sum(markers$p_val_adj == 0)
  num_pval1 <- sum(markers$p_val_adj == 1)
  num_significant <- sum(markers$p_val_adj < 0.05)
  num_upregulated <- sum(markers$avg_log2FC > 1)
  num_downregulated <- sum(markers$avg_log2FC < -1)
  
  cat("Number of genes with p_val_adj = 0:", num_pval0, "\n")
  cat("Number of genes with p_val_adj = 1:", num_pval1, "\n")
  cat("Number of significant genes (p_val_adj < 0.05):", num_significant, "\n")
  cat("Number of upregulated genes (avg_log2FC > 1):", num_upregulated, "\n")
  cat("Number of downregulated genes (avg_log2FC < -1):", num_downregulated, "\n")
}

3.2 Summarize Markers1 (markers_wilcox_RNA)

cat("Markers1 Summary (MAST with Batch Correction):\n")

Markers1 Summary (MAST with Batch Correction):

summarize_markers(markers_wilcox_RNA)

Number of genes with p_val_adj = 0: 3424 
Number of genes with p_val_adj = 1: 20820 
Number of significant genes (p_val_adj < 0.05): 15047 
Number of upregulated genes (avg_log2FC > 1): 7080 
Number of downregulated genes (avg_log2FC < -1): 16205 

3.3 Summary for Markers2 (markers_wilcox_SCT)

cat("Markers2 Summary (Wilcoxon Test):\n")

Markers2 Summary (Wilcoxon Test):

summarize_markers(markers_wilcox_SCT)

Number of genes with p_val_adj = 0: 4486 
Number of genes with p_val_adj = 1: 10140 
Number of significant genes (p_val_adj < 0.05): 15313 
Number of upregulated genes (avg_log2FC > 1): 14958 
Number of downregulated genes (avg_log2FC < -1): 2379 

4. Volcano Plots for All Genes

4.1 Volcano Plot for MAST with Batch Correction

EnhancedVolcano(markers_wilcox_RNA,
                lab = rownames(markers_wilcox_RNA),
                x = "avg_log2FC",
                y = "p_val_adj",
                title = "Wilcox with RNA assay (All Genes)",
                pCutoff = 0.05,
                FCcutoff = 1.0)

Warning: One or more p-values is 0. Converting to 10^-1 * current lowest non-zero p-value...

4.2 Volcano Plot for Wilcoxon Test

EnhancedVolcano(markers_wilcox_SCT,
                lab = rownames(markers_wilcox_SCT),
                x = "avg_log2FC",
                y = "p_val_adj",
                title = "Wilcoxon with SCT assay (All Genes)",
                pCutoff = 0.05,
                FCcutoff = 1.0)

Warning: One or more p-values is 0. Converting to 10^-1 * current lowest non-zero p-value...