Devevelopment of functions for formatting data and pedigree files for genetic analysis in Wombat Software

• Grant number: 24/19452-3
• Support Opportunities: Scholarships in Brazil - Scientific Initiation
• Start date: December 01, 2024
• End date: November 30, 2025
• Field of knowledge: Agronomical Sciences - Animal Husbandry - Genetics and Improvement of Domestic Animals
• Principal Investigator: Ricardo da Fonseca
• Grantee: Isabel Oliveira Silva
• Host Institution: Faculdade de Ciências Agrárias e Tecnológicas. Universidade Estadual Paulista (UNESP). Campus de Dracena. Dracena , SP, Brazil
• Associated research grant: 24/10028-4 - Improving Reproducibility of Results from Genetic Evaluation Analisys by Development of Data Formatting Functions for R Software, AP.R

Abstract

Recently, the concept of reproducibility of scientific results has gained importance, and practices to ensure it have been implemented in the most important scientific journals, which have begun to require the submission, along with the article, of the data used and, in a few cases, the scripts and routines utilized in the analysis procedures. Specifically, in the data formatting stage for genetic evaluation software, automation is possible and will contribute to minimizing errors in preparation and ensuring standardization of this stage, thereby increasing the chances of reproducibility of the final results by other research groups. Formatting the data according to the standards required by the software can, in some cases, involve many rules and demand significant time and attention to carry out. Errors at this stage can result in multiple files for the same dataset being worked on by different teams. In this scenario, the reproducibility of results is compromised, as the results could differ for the same data and analyses, preventing the verification of outcomes. To enable researchers to invest most of their time in interpreting results, minimize the inconveniences of file formatting, and ensure that results are consistent and of high quality, developing conversion functions for raw data files to the format required by the analysis software will be very helpful. Moreover, standardizing the formatting procedures carried out by these functions will enhance the prospects for reproducibility of results and simultaneously make the use of the software simpler and more efficient. The aim of this work will be to develop functions for converting raw files into the formats required by the Wombat software. The package to be developed will consist of a library of conversion functions for files (phenotypic data and pedigree) from a basic format to the format required by specific software for genetic and genomic studies. The functions will be developed using only the resources available in R itself and its packages. Initially, no function will be built in C++ (or another language) and encapsulated within an R function. Subsequently, the developed functions will be transformed into an R package. For the chosen software, functions will be developed to format phenotype and pedigree files for both univariate and multivariate analyses.