plotIBD

plotIBD visualizes sampled inheritance vectors in pedigrees to represent identity-by-descent sharing and support interpretation of linkage analysis for complex traits.

Key Features:

• Visualization of Inheritance Vectors: Plots sampled inheritance vectors to represent how chromosomal segments are co-inherited within pedigrees, aiding interpretation with missing data.
• Integration with Linkage Analysis: Identifies markers and relatives that co-inherit trait-associated chromosomal segments to complement parametric linkage analysis.
• Use of gl_auto and IBDgraph: Integrates inheritance sampling from gl_auto (MORGAN v3.0) and uses IBDgraph to identify classes of equivalent inheritance patterns.
• Analysis of Complex Traits: Borrows information across loci during parametric linkage analysis to explore the contributions of equivalence classes to linkage signals in general pedigrees.
• Haplotype Identification and Prioritization: Estimates identity-by-descent (IBD) sharing to identify haplotypes that tag linked segments and prioritize haplotype carriers for sequencing.

Scientific Applications:

• Genetic Research: Analyzing inheritance patterns of complex traits within family-based genetic studies.
• Linkage Analysis: Supporting interpretation of parametric linkage results by visualizing inheritance and equivalence-class contributions.
• Pedigree Studies: Deciphering complex inheritance patterns in large or general pedigrees.

Methodology:

Samples inheritance vectors using gl_auto (MORGAN v3.0) consistent with genotypic and pedigree data, applies IBDgraph to identify equivalent inheritance classes, plots the sampled inheritance vectors, estimates IBD sharing and identifies haplotypes, and borrows information across loci during parametric linkage analysis.