vqtl: An R Package for Mean-Variance QTL Mapping

Area of Science:

• Genetics
• Statistical Genetics
• Bioinformatics

Background:

• Quantitative trait loci (QTL) mapping typically focuses on the mean of a phenotype.
• Variance heterogeneity, influenced by QTL and covariates, can confound traditional QTL analysis.
• Existing methods often do not adequately address complex sources of variance.

Purpose of the Study:

• Introduce vqtl, an R package for comprehensive mean-variance QTL mapping.
• Develop a method to identify genetic loci affecting phenotype mean, variance, or both.
• Provide tools for robust QTL analysis that accounts for variance heterogeneity.

Main Methods:

• Implemented mean-variance QTL mapping in an R package (vqtl).
• Developed functions for genome scans, permutation testing for significance, and result visualization.
• Ensured interoperability with existing popular QTL analysis packages (e.g., qtl).

Main Results:

• vqtl allows simultaneous detection of mean QTL, variance QTL, and mean-variance QTL.
• The package effectively corrects for variance heterogeneity from both genetic and non-genetic factors.
• Provides a user-friendly interface for complex QTL analyses.

Conclusions:

• vqtl offers a powerful and flexible approach for genetic mapping of complex traits.
• The package facilitates the discovery of novel QTL by considering both mean and variance.
• Its design promotes adoption and re-analysis of existing genetic datasets.