AGHmatrix

AGHmatrix constructs relationship matrices from pedigree and molecular marker data to support genetic analyses such as estimation of breeding values, genome-wide association studies (GWAS), and population genetics.

Key Features:

• Pedigree matrix (A matrix): Constructs additive relationship matrices from pedigree information.
• Genomic matrix (G matrix): Builds genomic relationship matrices using molecular marker data.
• Combined matrix (H matrix): Integrates pedigree (A) and genomic (G) information to produce a corrected relationship matrix.
• Ploidy flexibility: Supports diploid and autopolyploid organisms for relationship matrix computation.
• Marker filtering: Includes functions to filter molecular markers for quality control.
• Pedigree checks: Provides routines to detect and check pedigree errors in large datasets.
• Implementation: Implemented as an R package for computational analyses.

Scientific Applications:

• Genomic estimated breeding values (GEBVs): Provides relationship matrices used for predicting GEBVs in breeding programs.
• Genome-wide association studies (GWAS): Supplies precise genetic relationship information to account for relatedness in association analyses.
• Population genetics: Enables investigation of population structure and dynamics through detailed relationship matrices.

Methodology:

Computes relationship matrices from pedigree and molecular marker data and integrates these sources to construct combined (H) matrices that correct inaccuracies arising from single-source matrices.