IntAssoPlot

IntAssoPlot integrates genome-wide association study (GWAS) P-values, gene structure, and linkage disequilibrium (LD) matrices into combined visualizations in an R package to support interpretation of association signals and identification of quantitative trait loci (QTL).

Key Features:

• Integrated visualization: Plots GWAS P-values on a -log10 scale together with gene structure and LD matrices in a single view.
• Flexible LD calculation: Allows plotting using LD matrices calculated from genotypic markers that differ from those used in the association analysis, including markers derived from DNA-Seq for RNA-Seq based GWAS.
• Publication-ready output: Produces figure-quality visualizations suitable for dissemination and publication.
• Biological insight extraction: Enables identification of loci exceeding genome-wide significance thresholds, nearby genes, and the extent of LD in selected regions.

Scientific Applications:

• QTL mapping and interpretation: Supports identification and contextualization of quantitative trait loci from GWAS results.
• LD and recombination analysis: Facilitates assessment of linkage disequilibrium and exploration of historical and evolutionary recombinations at the population level.
• Gene-contextualized association analysis: Enables evaluation of association signals in the context of gene structure to prioritize candidate genes near significant loci.

Methodology:

Creates a main-panel plot that links GWAS P-values on a -log10 scale with gene structure and LD matrices via connecting lines and can use LD matrices calculated from alternative genotypic marker sets (e.g., DNA-Seq markers distinct from association markers).