trio

trio provides functions in R within the Bioconductor ecosystem for analysis of case-parent trio genetic data, including computation of linkage disequilibrium measures, genotype imputation, simulation of SNP-interaction disease risk, setup of matched case pseudo-control data for logic regression, and power and sample-size calculations.

Key Features:

• Linkage Disequilibrium (LD) Analysis: Computes pairwise LD measures and identifies LD blocks to delineate genomic regions with high linkage.
• Trio Logic Regression Setup: Constructs matched case pseudo-control genotype data specifically for case-parent trios to support logic regression analyses.
• Genotype Imputation: Imputes missing genotypes in trio datasets to improve data completeness for downstream analyses.
• Simulation of Case-Parent Trios: Simulates case-parent trios with disease risk models that depend on SNP interactions.
• Power and Sample Size Calculation: Performs power and sample size calculations tailored to trio study designs.

Scientific Applications:

• Family-based genetic association studies: Supports analysis of case-parent trios to detect genetic associations while controlling for population stratification.
• Inheritance pattern analysis: Enables investigation of transmission patterns and intra-family variant interactions.
• Simulation of genetic disease models: Facilitates generation of simulated trio datasets to evaluate SNP interaction effects on disease risk.
• Study design and power estimation: Aids in designing trio-based studies by providing power and sample-size calculations.

Methodology:

Analyses and functions are implemented in R and operate within the Bioconductor framework.