Pedixplorer: a Bioconductor package to streamline pedigree design and visualization

Area of Science:

• Genetics
• Bioinformatics
• Computational Biology

Background:

• Kinship analysis is crucial for genetic research, including linkage studies and population genetics.
• Existing tools like the kinship2 package require updates for handling large, complex pedigrees with features like inbreeding loops.
• There is a need for flexible, user-friendly software to manage and analyze intricate pedigree data, especially in areas like animal breeding.

Purpose of the Study:

• To introduce Pedixplorer, a novel Bioconductor package designed to advance kinship analyses.
• To provide enhanced functionality for managing and visualizing large, complex pedigrees, including those with inbreeding loops.
• To offer a user-friendly interface, including a Shiny application, for both R and non-R users.

Main Methods:

• Development of the Pedixplorer package, built on Bioconductor standards and modern programming practices.
• Implementation of an S4 Pedigree object for efficient representation of complex pedigrees.
• Creation of new functions for automatic pedigree querying, filtering, and trimming, alongside rewritten graphical functions for improved visualization customization.
• Development of a comprehensive Shiny application for accessible pedigree creation, filtering, and customization.

Main Results:

• Pedixplorer provides an S4 Pedigree object for efficient handling of complex pedigrees.
• New functions allow for automated querying, filtering, and trimming of large pedigrees.
• Rewritten graphical functions enhance pedigree visualization customization.
• A user-friendly Shiny application is available for local use and via a dedicated website, enabling non-R users to manage pedigrees.

Conclusions:

• Pedixplorer offers a modern, flexible, and user-friendly solution for kinship analysis, particularly for large and complex pedigrees.
• The package enhances existing capabilities and provides new tools for efficient pedigree data management and visualization.
• The integrated Shiny application broadens accessibility for researchers and users with varying levels of R proficiency.