Pedixplorer

Pedixplorer handles family data through an S4 Pedigree object to create correlation structures describing family relationships such as kinship and identity-by-descent for use in mixed effects models, with integrated functions for pedigree querying, filtering, trimming, and visualization.

Key Features:

• Pedigree Object: Core S4 Pedigree object facilitates efficient representation of complex pedigrees including large multigeneration complex pedigrees with inbreeding loops.
• Kinship and Identity-by-Descent Computation: Creates correlation structures describing family relationships such as kinship and identity-by-descent for modeling family data in mixed effects models such as in the coxme function.
• X Chromosome Kinship: Computes kinship for the X chromosome.
• Pedigree Trimming: Utilities to trim the Pedigree object with various criteria.
• Pedigree Drawing: Graphical functions for pedigree visualization focused on producing compact layouts without intervention, rewritten for better customization.
• Automatic Querying and Filtering: New functions enable automatic querying, filtering, and trimming of large pedigrees.

Scientific Applications:

• Genetic Linkage Studies: Pedigree design and analysis for genetic linkage studies where understanding kinship relationships is fundamental.
• Population Genetics: Analysis of kinship relationships in population genetics research.
• Domestic Animal Breeding: Handling of large multigeneration complex pedigrees with inbreeding loops frequently seen in domestic animal breeding.
• Mixed Effects Modeling: Modeling family data in mixed effects models using kinship and identity-by-descent correlation structures.

Methodology:

Pedixplorer builds upon the foundation of kinship2, integrating Bioconductor standards and recent programming practices. The package creates correlation structures for kinship and identity-by-descent that can be used in mixed effects models, with rewritten graphical functions for pedigree visualization and utilities for pedigree trimming based on various criteria.