methrix

methrix processes whole-genome bisulfite sequencing (WGBS) bedGraph-like coverage files to summarize CpG-level DNA methylation, aggregate methylation and coverage matrices, and enable downstream differential methylation (DMR) analysis.

Key Features:

• Comprehensive File Reading: Reader for bedGraph or tab-separated coverage files that summarizes methylation calls using annotated reference indices, infers and collapses strands, and handles uncovered reference CpG sites.
• Data Aggregation: Aggregates multiple bedGraph files into cohesive methylation and coverage matrices for downstream analyses.
• Quality Control and Subsetting: Provides functions for quality-control filtering and subsetting of methylation and coverage data.
• Visualization: Includes visualization functions for interpreting methylation and coverage patterns.
• DMR Integration: Facilitates integration with differentially methylated region (DMR) calling and annotation tools.
• R/Bioconductor Implementation: Implemented in R with compatibility for the Bioconductor ecosystem.

Scientific Applications:

• Epigenome-Wide Association Studies (EWAS): Supports processing and aggregation of WGBS data for EWAS to detect methylation–phenotype associations.
• Developmental Biology: Enables analysis of CpG methylation changes across developmental stages.
• Cancer Research: Enables analysis of genome-wide methylation alterations associated with cancer.

Methodology:

Reads bedGraph-like coverage files and summarizes methylation calls using annotated reference indices with strand inference and collapse, handles uncovered CpG sites, aggregates files into methylation/coverage matrices, and performs quality-control filtering, subsetting, visualization, and integration for DMR calling. The package is implemented in R and is compatible with the Bioconductor ecosystem.