ramr

ramr identifies aberrantly methylated DNA regions (AMRs) in large DNA methylation datasets obtained by array or high-throughput methylation sequencing, with applications for detecting rare epimutations associated with disease risk.

Key Features:

• AMR Detection: Identifies infrequent aberrant DNA methylation events (epimutations) in large-scale methylation data from array or next-generation sequencing platforms.
• Visualization: Provides functions to visualize found aberrantly methylated regions.
• Reference Set Generation: Generates sets of all possible regions for use as reference sets in enrichment analysis.
• Test Data Simulation: Generates biologically relevant test datasets for performance evaluation of AMR/DMR search algorithms.
• Functional Annotation: Supports functional annotation of AMRs arising at early developmental stages.

Scientific Applications:

• Cancer Risk Assessment: Discovers AMRs associated with elevated risk of colorectal cancer and other cancers.
• Constitutional Epimutation Detection: Analyzes rare alterations transmitted mitotically or transgenerationally that occur at low mosaic levels and may confer disease risk later in life.
• Large Public Dataset Analysis: Applicable for analysis of large public methylation datasets.
• Early Developmental Studies: Identifies and functionally annotates AMRs arising at early developmental stages.

Methodology:

The method assesses accuracy and performance metrics for detecting aberrantly methylated regions in methylation data obtained by array or next-generation sequencing techniques.