Getting started

• 1. Read data and get beta values
  • 1.1. Read .idat files
    • 1.1.1. Download test data
    • 1.1.2. Define and read annotation
    • 1.1.3. Read samples .idat
    • 1.1.4. Save pylluminator samples (optional)
  • 1.2. Calculate and plot beta values
  • 1.3. Preprocessing
  • 1.4. Data insights
• 2. Sample quality control
  • 2.1. Load pylluminator Samples
  • 2.2. Chose a sample and print QCs
  • 2.3. Plot the number of beads per probe
• 3. DMPs and DMRs
  • 3.1. Load pylluminator Samples
  • 3.2. Differentially Methylated Probes
  • 3.3. Differentially Methylated Regions
  • 3.4. Gene visualization
• 4. Copy Number Variation
  • 4.1. Load pylluminator Samples
  • 4.2. Get CNVs for a sample group
  • 4.3. Visualize CNVs and segments
• 5. Pathway analysis
  • 5.1. Data preparation
    • 5.1.1. Gene set selection
    • 5.1.2. Organism specification
  • 5.2. Over-Representation Analysis
    • 5.2.1. ORA without background
    • 5.2.2. ORA with background
  • 5.3. Pre-rank GSEA
  • 5.4. GSEA