AGHmatrix: genetic relationship matrices in R

Area of Science:

• Genetics
• Ecology
• Bioinformatics

Background:

• Understanding genetic relationships is crucial for geneticists and ecologists.
• These relationships inform studies on phenotypic variation, fitness, and population dynamics.

Purpose of the Study:

• Introduce AGHmatrix, an R package for constructing genetic relationship matrices.
• Facilitate the estimation of genetic relationships using pedigree and molecular marker data.

Main Methods:

• The AGHmatrix package constructs pedigree (A), molecular marker (G), and combined (H) matrices.
• It supports any ploidy level and includes functions for marker filtering and pedigree error checking.
• Relationship matrices can be computed from pedigree, genomic data, or a combination of both.

Main Results:

• AGHmatrix enables the creation of A, G, and H matrices for relationship estimation.
• The software handles diverse ploidy levels and offers tools for data quality control.
• Outputs are applicable to genomic prediction and genome-wide association studies.

Conclusions:

• AGHmatrix provides a robust R package for calculating genetic relationships.
• Its functionalities support advanced genetic analyses in various biological contexts.