wtest

wtest performs association testing and integrated genetic epistasis analysis to identify main effects and pairwise and higher-order interactions among SNPs and CpG sites in GWAS and epigenome-wide datasets.

Key Features:

• Association testing for main effects: Provides statistical association testing for single-marker (SNP and CpG) main effects in genome-wide and epigenome-wide data.
• Pairwise and high-order interaction testing: Supports testing of pairwise and higher-order interactions among genomic features.
• SNP-SNP and SNP-CpG interaction analysis: Enables analysis of SNP-SNP and SNP-CpG interactions to assess epistatic relationships.
• Cis-regulation analysis: Performs cis-regulation analysis of SNP and CpG sites across genome-wide and epigenome-wide datasets.
• Integrated genetic epistasis framework: Implements a statistical framework for integrated genetic epistasis testing across large-scale datasets.
• Computational efficiency: Addresses computational challenges associated with genome-wide interaction analysis to improve scalability.
• Post-test diagnostics and analytics: Includes post-test diagnostic and analytical functions to assess reliability and interpretability of results.

Scientific Applications:

• Epistasis detection in GWAS: Identifies pairwise and higher-order epistatic interactions among SNPs in genome-wide association studies.
• SNP-CpG interaction studies: Detects interactions between genetic variants and DNA methylation (CpG) sites in epigenome-wide analyses.
• Cis-regulatory investigations: Examines cis-regulation between SNPs and CpG sites to study local regulatory effects.
• Elucidating genetic architecture of disease: Supports exploration of complex genetic interactions that may contribute to human disease etiology.

Methodology:

Performs association testing for main effects and for pairwise and high-order interactions using an integrated statistical framework for genetic epistasis and provides post-test diagnostic and analytical functions.