Pedixplorer: A modern R BioConductor package for efficient kinship analysis to draw and request complex pedigrees
Author(s): Louis Le Nézet,Jason Sinnwell,Pascale Quignon,Catherine André
Affiliation(s): 1 CNRS - UR1, ERL Inserm U1305 - UMR6290 IGDR (Institut de Génétique et Développement de Rennes) - 35000 Rennes, France
Understanding kinship relationships is fundamental in genetic studies, particularly in pedigree analysis in genetic linkage studies and population genetics. The legacy “kinship2” CRAN package has been a cornerstone in this area; however, with its unmaintained status and evolving needs in bioinformatics, arises a necessity for an updated, flexible toolset and user-friendly application. To address this gap, we present “Pedixplorer,” a novel Bioconductor package designed to facilitate comprehensive kinship analyses with enhanced functionality and usability. Built upon the robust foundation of “Kinship2,” Pedixplorer harnesses its core functionalities while integrating modern programming practices and Bioconductor standards. Its central component is the “Pedigree” S4 object, enabling efficient representation of complex pedigree structures, such as mono- and di-zygotic twins or spouses. It also contains all the information needed to customize and design the pedigree graphic representation. Key highlights of Pedixplorer include: - Pedigree Creation and Management: Simplified data input and manipulation for pedigrees of varying complexity from dataframe and automatic errors detection and resolution. - Kinship Calculation: Accurate and scalable kinship coefficient estimation for relatedness analysis. - Informativeness Computation and Filtering: Customizable selection of probands and filtering of their relatives according to distance. - Visualization: Enhanced plotting capabilities and customization for intuitive pedigree exploration. The package's intuitive interface and extensive documentation make it accessible to both novice and experienced users in the field of genetic research. An RShiny application will soon be available to further enhance user experience. By presenting Pedixplorer at EuroBioC2024, we aim to showcase its utility in handling, for example, large dog pedigrees and demonstrate how it streamlines data management and analysis in genetic studies. We invite collaboration and feedback from the Bioconductor community to enhance Pedixplorer and support its adoption in pedigree-based genetic research workflows.