{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,8]],"date-time":"2026-04-08T21:49:59Z","timestamp":1775684999975,"version":"3.50.1"},"reference-count":25,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2023,7,20]],"date-time":"2023-07-20T00:00:00Z","timestamp":1689811200000},"content-version":"vor","delay-in-days":19,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"UF royalty"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad445","type":"journal-article","created":{"date-parts":[[2023,7,20]],"date-time":"2023-07-20T00:49:14Z","timestamp":1689814154000},"source":"Crossref","is-referenced-by-count":84,"title":["AGHmatrix: genetic relationship matrices in R"],"prefix":"10.1093","volume":"39","author":[{"given":"Rodrigo R","family":"Amadeu","sequence":"first","affiliation":[{"name":"Bayer U.S.\u2014Crop Science , Chesterfield, MO, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0634-3277","authenticated-orcid":false,"given":"Antonio Augusto F","family":"Garcia","sequence":"additional","affiliation":[{"name":"Departamento de Gen\u00e9tica, Escola Superior de Agricultura Luiz de Queiroz, Universidade de S\u00e3o Paulo , Piracicaba, SP, Brazil"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8973-9351","authenticated-orcid":false,"given":"Patricio R","family":"Munoz","sequence":"additional","affiliation":[{"name":"Blueberry, Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida , Gainesville, FL 32611, United States"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9655-4838","authenticated-orcid":false,"given":"Lu\u00eds Felipe V","family":"Ferr\u00e3o","sequence":"additional","affiliation":[{"name":"Blueberry, Breeding and Genomics Lab, Horticultural Sciences Department, University of Florida , Gainesville, FL 32611, United States"}]}],"member":"286","published-online":{"date-parts":[[2023,7,20]]},"reference":[{"key":"2023072623205302800_btad445-B1","doi-asserted-by":"crossref","first-page":"4","DOI":"10.3835\/plantgenome2016.01.0009","article-title":"AGHmatrix: r package to construct relationship matrices for autotetraploid and diploid species: a blueberry example","volume":"9","author":"Amadeu","year":"2016","journal-title":"Plant Genome"},{"key":"2023072623205302800_btad445-B2","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1007\/s00122-015-2607-9","article-title":"Estimating genomic heritabilities at the level of family-Pool samples of perennial ryegrass using genotyping-by-sequencing","volume":"129","author":"Ashraf","year":"2016","journal-title":"Theor Appl Genet"},{"key":"2023072623205302800_btad445-B3","author":"Butler","year":"2017"},{"key":"2023072623205302800_btad445-B500","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1093\/genetics\/39.6.859","article-title":"An extension of the concept of partitioning hereditary variance for analysis of covariances among relatives when epistasis is present","volume":"39","author":"Cockerham","year":"1954","journal-title":"Genetics"},{"key":"2023072623205302800_btad445-B4","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1534\/g3.119.400059","article-title":"Genomic prediction of autotetraploids; influence of relationship matrices, allele dosage, and continuous genotyping calls in phenotype prediction","volume":"9","author":"de Bem Oliveira","year":"2019","journal-title":"G3 (Bethesda)"},{"key":"2023072623205302800_btad445-B5","doi-asserted-by":"crossref","first-page":"250","DOI":"10.3835\/plantgenome2011.08.0024","article-title":"Ridge regression and other kernels for genomic selection with R package rrBLUP","volume":"4","author":"Endelman","year":"2011","journal-title":"The Plant Genome"},{"key":"2023072623205302800_btad445-B6","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1534\/genetics.118.300685","article-title":"Genetic variance partitioning and genome-wide prediction with allele dosage information in autotetraploid potato","volume":"209","author":"Endelman","year":"2018","journal-title":"Genetics"},{"key":"2023072623205302800_btad445-B7","doi-asserted-by":"crossref","first-page":"69","DOI":"10.2307\/2529339","article-title":"A simple method for computing the inverse of a numerator relationship matrix used in prediction of breeding values","volume":"32","author":"Henderson","year":"1976","journal-title":"Biometrics"},{"key":"2023072623205302800_btad445-B8","doi-asserted-by":"crossref","first-page":"1271","DOI":"10.1007\/s00122-012-1785-y","article-title":"Use of the numerator relationship matrix in genetic analysis of autopolyploid species","volume":"124","author":"Kerr","year":"2012","journal-title":"Theor Appl Genet"},{"key":"2023072623205302800_btad445-B9","doi-asserted-by":"crossref","first-page":"4656","DOI":"10.3168\/jds.2009-2061","article-title":"A relationship matrix including full pedigree and genomic information","volume":"92","author":"Legarra","year":"2009","journal-title":"J Dairy Sci"},{"key":"2023072623205302800_btad445-B10","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12711-020-00568-0","article-title":"Weighted single-step genomic best linear unbiased prediction integrating variants selected from sequencing data by association and bioinformatics analyses","volume":"52","author":"Liu","year":"2020","journal-title":"Genet Sel Evol"},{"key":"2023072623205302800_btad445-B11","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1186\/s12711-018-0386-x","article-title":"The effect of the H\u22121 scaling factors \u03c4 and \u03c9 on the structure of H in the single-step procedure","volume":"50","author":"Martini","year":"2018","journal-title":"Genet Sel Evol"},{"key":"2023072623205302800_btad445-B12","doi-asserted-by":"crossref","first-page":"4648","DOI":"10.3168\/jds.2009-2064","article-title":"Computing procedures for genetic evaluation including phenotypic, full pedigree, and genomic information","volume":"92","author":"Misztal","year":"2009","journal-title":"J Dairy Sci"},{"key":"2023072623205302800_btad445-B13","article-title":"Linear models for the prediction of animal breeding values","author":"Mrode","year":"2014","journal-title":"Cabi"},{"key":"2023072623205302800_btad445-B14","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.2135\/cropsci2012.12.0673","article-title":"Genomic relationship matrix for correcting pedigree errors in breeding populations: impact on genetic parameters and genomic selection accuracy","volume":"54","author":"Munoz","year":"2014","journal-title":"Crop Science"},{"key":"2023072623205302800_btad445-B15","doi-asserted-by":"crossref","DOI":"10.3835\/plantgenome2015.08.0073","article-title":"Software for genome-wide association studies in autopolyploids and its application to potato","volume":"9","author":"Rosyara","year":"2016","journal-title":"Plant Genome"},{"key":"2023072623205302800_btad445-B1600","doi-asserted-by":"crossref","first-page":"809","DOI":"10.1007\/s00122-013-2258-7","article-title":"Improving the analysis of low heritability complex traits for enhanced genetic gain in potato","volume":"127","author":"Slater","year":"2014","journal-title":"Theoretical and applied genetics"},{"key":"2023072623205302800_btad445-B16","doi-asserted-by":"crossref","DOI":"10.3835\/plantgenome2016.02.0021","article-title":"Improving genetic gain with genomic selection in autotetraploid potato","volume":"9","author":"Slater","year":"2016","journal-title":"Plant Genome"},{"key":"2023072623205302800_btad445-B17","doi-asserted-by":"crossref","first-page":"6547","DOI":"10.3168\/jds.2014-8210","article-title":"Comparison of genomic predictions using genomic relationship matrices built with different weighting factors to account for locus-specific variances","volume":"97","author":"Su","year":"2014","journal-title":"J Dairy Sci"},{"key":"2023072623205302800_btad445-B18","author":"Su","year":"2012"},{"key":"2023072623205302800_btad445-B19","doi-asserted-by":"crossref","first-page":"4414","DOI":"10.3168\/jds.2007-0980","article-title":"Efficient methods to compute genomic predictions","volume":"91","author":"VanRaden","year":"2008","journal-title":"J Dairy Sci"},{"key":"2023072623205302800_btad445-B20","doi-asserted-by":"crossref","first-page":"1223","DOI":"10.1534\/genetics.113.155176","article-title":"On the additive and dominant variance and covariance of individuals within the genomic selection scope","volume":"195","author":"Vitezica","year":"2013","journal-title":"Genetics"},{"key":"2023072623205302800_btad445-B21","volume-title":"Evolution and Selection of Quantitative Traits","author":"Walsh","year":"1998"},{"key":"2023072623205302800_btad445-B22","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1111\/j.1365-2656.2009.01639.x","article-title":"An ecologist\u2019s guide to the animal model","volume":"79","author":"Wilson","year":"2010","journal-title":"J Anim Ecol"},{"key":"2023072623205302800_btad445-B23","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1038\/ng.608","article-title":"Common SNPs explain a large proportion of the heritability for human height","volume":"42","author":"Yang","year":"2010","journal-title":"Nat Genet"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/advance-article-pdf\/doi\/10.1093\/bioinformatics\/btad445\/50918236\/btad445.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/7\/btad445\/50970525\/btad445.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/39\/7\/btad445\/50970525\/btad445.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,26]],"date-time":"2023-07-26T23:21:31Z","timestamp":1690413691000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/doi\/10.1093\/bioinformatics\/btad445\/7227072"}},"subtitle":[],"editor":[{"given":"Russell","family":"Schwartz","sequence":"additional","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2023,7,1]]},"references-count":25,"journal-issue":{"issue":"7","published-print":{"date-parts":[[2023,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btad445","relation":{},"ISSN":["1367-4811"],"issn-type":[{"value":"1367-4811","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,7,1]]},"published":{"date-parts":[[2023,7,1]]},"article-number":"btad445"}}