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AGHmatrix: genetic relationship matrices in R
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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10371492/ https://www.ncbi.nlm.nih.gov/pubmed/37471595 http://dx.doi.org/10.1093/bioinformatics/btad445 |
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author | Amadeu, Rodrigo R Garcia, Antonio Augusto F Munoz, Patricio R Ferrão, Luís Felipe V |
author_facet | Amadeu, Rodrigo R Garcia, Antonio Augusto F Munoz, Patricio R Ferrão, Luís Felipe V |
author_sort | Amadeu, Rodrigo R |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-10371492 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-103714922023-07-27 AGHmatrix: genetic relationship matrices in R Amadeu, Rodrigo R Garcia, Antonio Augusto F Munoz, Patricio R Ferrão, Luís Felipe V Bioinformatics Applications Note 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. Oxford University Press 2023-07-20 /pmc/articles/PMC10371492/ /pubmed/37471595 http://dx.doi.org/10.1093/bioinformatics/btad445 Text en © The Author(s) 2023. Published by Oxford University Press. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Applications Note Amadeu, Rodrigo R Garcia, Antonio Augusto F Munoz, Patricio R Ferrão, Luís Felipe V AGHmatrix: genetic relationship matrices in R |
title | AGHmatrix: genetic relationship matrices in R |
title_full | AGHmatrix: genetic relationship matrices in R |
title_fullStr | AGHmatrix: genetic relationship matrices in R |
title_full_unstemmed | AGHmatrix: genetic relationship matrices in R |
title_short | AGHmatrix: genetic relationship matrices in R |
title_sort | aghmatrix: genetic relationship matrices in r |
topic | Applications Note |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10371492/ https://www.ncbi.nlm.nih.gov/pubmed/37471595 http://dx.doi.org/10.1093/bioinformatics/btad445 |
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