SNPAssoc

SNPAssoc performs statistical association analyses of single nucleotide polymorphisms (SNPs) to identify genetic variants and haplotypes associated with complex traits and diseases.

Key Features:

• Automation of SNP analysis: Automates whole-genome SNP analyses including computation of descriptive statistics and exploratory analysis of missing values.
• Hardy-Weinberg equilibrium: Calculates Hardy–Weinberg equilibrium for SNP genotype frequencies.
• Association analysis using GLMs: Performs association testing via generalized linear models for quantitative and binary traits.
• Haplotype and epistasis analysis: Conducts multi-SNP haplotype analyses and epistasis (gene–gene interaction) analysis.
• R integration and haplo.stats extension: Implemented in R using S4 classes and extends the haplo.stats package.

Scientific Applications:

• Genetic association studies: Identification and analysis of SNPs, haplotypes, and gene–gene interactions contributing to complex disease susceptibility and quantitative traits.

Methodology:

Computes descriptive statistics and missing-value exploration, performs Hardy–Weinberg tests, association testing with generalized linear models for quantitative and binary traits, and executes haplotype and epistasis analyses; implemented in R using S4 classes and extending haplo.stats.