Methylation Variability Analysis

关于

Provides a comprehensive R-based workflow for analyzing whole-genome bisulfite sequencing (WGBS) data to identify highly variable CpGs (HVCs) and explore epigenetic heterogeneity across biological samples. By leveraging the methylKit package, it automates the creation of multi-sample methylation matrices, computes key variability metrics like variance and coefficient of variation, and generates high-quality visualizations including heatmaps and distribution plots. This skill is ideal for researchers looking to uncover dynamic epigenetic loci and compare heterogeneity between different disease states, cell types, or experimental conditions.

主要功能

• Automates multi-sample CpG methylation matrix construction from WGBS coverage files.
• Generates visualizations such as methylation heatmaps and mean-vs-variance scatter plots.
• Identifies Highly Variable CpGs (HVCs) as candidate loci for epigenetic heterogeneity.
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• Calculates variability statistics including variance, Median Absolute Deviation (MAD), and Coefficient of Variation (CV).
• Includes customizable filtering for coverage and dataset-specific variability thresholds.

使用场景

• Identifying highly variable methylation markers across different cell types or replicates.
• Quantifying biological noise and stochastic methylation changes in WGBS datasets.
• Comparing epigenetic heterogeneity between disease samples and healthy controls.