IMAGE_R

IMAGE_R maps methylation quantitative trait loci (mQTLs) in bisulfite sequencing data to detect genetic variants associated with DNA methylation variation.

Key Features:

• Statistical methodology: Employs a statistical model tailored for mQTL mapping that accommodates the count nature of bisulfite sequencing data.
• Allele-specific analysis: Integrates allele-specific methylation patterns from heterozygous individuals to increase precision and power of mQTL detection.
• Comparative performance: Demonstrates, via extensive simulation studies, identification of a greater number of mQTLs compared with other existing approaches.
• R package implementation: Provided as an implementation in R for analysis of sequencing-based methylation data.

Scientific Applications:

• mQTL mapping: Applied to bisulfite sequencing studies to map genetic variants associated with DNA methylation levels.
• Genotype–epigenotype associations: Used to elucidate interactions between genetic variants and allele-specific DNA methylation that may influence genotype–trait associations.
• Epigenetic studies of traits and disease: Facilitates investigation of epigenetic mechanisms underlying phenotypic traits and diseases.

Methodology:

Models the count-based nature of bisulfite sequencing data and integrates allele-specific methylation from heterozygous individuals, with performance assessed through extensive simulation studies.