ggroups

ggroups computes genetic group contributions and constructs additive and dominance genetic relationship matrices and their inverses from pedigree data to support quantitative genetics analyses.

Key Features:

• Pedigree Data Management: Functions to check and process pedigree data for integrity and preparation for downstream analyses.
• Genetic Relationship Matrices: Calculation of additive and dominance genetic relationship matrices and their inverses.
• Matrix Formats: Support for matrix and tabular-sparse formats for relationship matrix calculations.
• Genetic Group Contributions (Q Matrix): Computation of the matrix of genetic group contributions (Q) to address unequal average genetic merits among groups with unknown parents.
• Computational Optimization: Optimized implementations, including options for parallel processing, to improve performance for large pedigrees and numerous genetic groups.

Scientific Applications:

• Population Structure Analysis: Assessing genetic relationships and population structure using relationship matrices.
• Genetic Merit Prediction: Supporting prediction of genetic merit using additive and dominance relationship matrices.
• Animal Breeding Studies: Managing datasets with partially unknown parentage via genetic groups to refine genetic merit estimates across groups.

Methodology:

Efficient processing and validation of pedigree data; optimized algorithms for computing genetic relationship matrices and their inverses; and implementation of parallel computing techniques for computationally intensive tasks.