Pedixplorer: a Bioconductor package to streamline pedigree design and visualization.

Abstract

Motivation: Understanding kinship relationships is fundamental to genetic research, particularly in the context of genetic linkage studies and population genetics. Pedigree design and analysis are a prerequisite for these investigations. The legacy kinship2 CRAN package has been a cornerstone in this area; however, the need for handling larger and more complex datasets necessitates an updated, flexible, and user-friendly toolset. To address this issue, we present Pedixplorer, a novel Bioconductor package designed to enhance kinship analyses with modern functionality and usability, especially in large multigeneration complex pedigrees with inbreeding loops, which are frequently seen in domestic animal breeding.

Results: Pedixplorer builds upon the robust foundation of kinship2, integrating Bioconductor standards and most recent programming practices. Its core component is the S4 Pedigree object, facilitating efficient representation of complex pedigrees. The new functions enable automatic querying, filtering, and trimming of large pedigrees, while the graphical functions have been rewritten for better customization in pedigree visualizations. Additionally, Pedixplorer offers a comprehensive Shiny application, accessible both locally and via a dedicated website, allowing non-R users to easily create, filter, and customize pedigrees.

Availability and implementation: The Pedixplorer package is freely available at: https://www.bioconductor.org/packages/release/bioc/html/Pedixplorer.html with additional documentation at https://louislenezet.github.io/Pedixplorer. A user-friendly web application is available at: https://pedixplorer.univ-rennes.fr.