gJLS2

gJLS2 performs generalized joint location and scale analysis to detect genetic variants that influence both the mean and the variance of quantitative traits in genome-wide association studies (GWAS).

Key Features:

• Generalized joint testing: Implements joint tests of location (mean) and scale (variance) effects in GWAS to evaluate both components simultaneously.
• R package implementation: Provided as an R package for programmatic use within R-based analysis workflows.
• Complex data support: Handles related samples, genotype dosage data, and analyses on the X chromosome.
• Integration with analysis tools: Can be invoked from PLINK or used within scripting environments for genome-wide analyses.
• Data-level flexibility and scalability: Applicable to individual-level and summary-level data and designed to accommodate large-scale biobank datasets.

Scientific Applications:

• Enhanced marker discovery: Increases ability to detect genome-wide signals, including variants affecting trait variance and signals relevant to gene–environment interactions, and aids prioritization of candidate markers.
• Standardized reporting of results: Supports standardized reporting of P-values from joint location-and-scale analyses to improve transparency and reproducibility in genetic studies.

Methodology:

Implements generalized statistical methods performing joint tests of location (mean) and scale (variance) in GWAS, explicitly supporting related individuals, genotype dosages, X-chromosome analyses, and operation on both individual-level and summary-level data.