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. 2023 Jul 1;39(7):btad445.
doi: 10.1093/bioinformatics/btad445.

AGHmatrix: genetic relationship matrices in R

Rodrigo R Amadeu  1 , Antonio Augusto F Garcia  2 , Patricio R Munoz  3 , Luís Felipe V Ferrão  3
Affiliations

AGHmatrix: genetic relationship matrices in R

Rodrigo R Amadeu et al. Bioinformatics. .

Abstract

Motivation: The resemble between relatives computed from pedigree and genomic data is an important resource for geneticists and ecologists, who are interested in understanding how genes influence phenotypic variation, fitness adaptation, and population dynamics.

Results: The AGHmatrix software is an R package focused on the construction of pedigree (A matrix) and/or molecular markers (G matrix), with the possibility of building a combined matrix of pedigree corrected by molecular markers (H matrix). Designed to estimate the relationships for any ploidy level, the software also includes auxiliary functions related to filtering molecular markers, and checks pedigree errors in large data sets. After computing the relationship matrices, results from the AGHmatrix can be used in different contexts, including on prediction of (genomic) estimated breeding values and genome-wide association studies.

Availability and implementation: AGHmatrix v2.1.0 is available under GPL-3 license in CRAN at https://cran.r-project.org/web/packages/AGHmatrix/index.html and also in GitHub at https://github.com/rramadeu/AGHmatrix. It has a comprehensive tutorial, and it follows with real data examples.

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Conflict of interest statement

None declared.

Figures

Figure 1.
Figure 1.
(a) RAM usage at the peak and (b) time to build A matrix for different sizes of pedigree
See this image and copyright information in PMC

References

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    1. de Bem Oliveira I, Resende MF Jr, Ferrão LFV et al. Genomic prediction of autotetraploids; influence of relationship matrices, allele dosage, and continuous genotyping calls in phenotype prediction. G3 (Bethesda) 2019;9:1189–98. - PMC - PubMed

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