rBahadur: efficient simulation of structured high-dimensional genotype data with applications to assortative mating

Existing methods for generating synthetic genotype data are ill-suited for replicating the effects of assortative mating (AM). We propose rb_dplr, a novel and computationally efficient algorithm for generating high-dimensional binary random variates that effectively recapitulates AM-induced genetic...

Descripción completa

Detalles Bibliográficos
Autores principales: Border, Richard, Malik, Osman Asif
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10439545/
https://www.ncbi.nlm.nih.gov/pubmed/37596553
http://dx.doi.org/10.1186/s12859-023-05442-6
_version_ 1785092969255141376
author Border, Richard
Malik, Osman Asif
author_facet Border, Richard
Malik, Osman Asif
author_sort Border, Richard
collection PubMed
description Existing methods for generating synthetic genotype data are ill-suited for replicating the effects of assortative mating (AM). We propose rb_dplr, a novel and computationally efficient algorithm for generating high-dimensional binary random variates that effectively recapitulates AM-induced genetic architectures using the Bahadur order-2 approximation of the multivariate Bernoulli distribution. The rBahadur R library is available through the Comprehensive R Archive Network at https://CRAN.R-project.org/package=rBahadur. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-023-05442-6.
format Online
Article
Text
id pubmed-10439545
institution National Center for Biotechnology Information
language English
publishDate 2023
publisher BioMed Central
record_format MEDLINE/PubMed
spelling pubmed-104395452023-08-20 rBahadur: efficient simulation of structured high-dimensional genotype data with applications to assortative mating Border, Richard Malik, Osman Asif BMC Bioinformatics Software Existing methods for generating synthetic genotype data are ill-suited for replicating the effects of assortative mating (AM). We propose rb_dplr, a novel and computationally efficient algorithm for generating high-dimensional binary random variates that effectively recapitulates AM-induced genetic architectures using the Bahadur order-2 approximation of the multivariate Bernoulli distribution. The rBahadur R library is available through the Comprehensive R Archive Network at https://CRAN.R-project.org/package=rBahadur. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-023-05442-6. BioMed Central 2023-08-18 /pmc/articles/PMC10439545/ /pubmed/37596553 http://dx.doi.org/10.1186/s12859-023-05442-6 Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Software
Border, Richard
Malik, Osman Asif
rBahadur: efficient simulation of structured high-dimensional genotype data with applications to assortative mating
title rBahadur: efficient simulation of structured high-dimensional genotype data with applications to assortative mating
title_full rBahadur: efficient simulation of structured high-dimensional genotype data with applications to assortative mating
title_fullStr rBahadur: efficient simulation of structured high-dimensional genotype data with applications to assortative mating
title_full_unstemmed rBahadur: efficient simulation of structured high-dimensional genotype data with applications to assortative mating
title_short rBahadur: efficient simulation of structured high-dimensional genotype data with applications to assortative mating
title_sort rbahadur: efficient simulation of structured high-dimensional genotype data with applications to assortative mating
topic Software
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10439545/
https://www.ncbi.nlm.nih.gov/pubmed/37596553
http://dx.doi.org/10.1186/s12859-023-05442-6
work_keys_str_mv AT borderrichard rbahadurefficientsimulationofstructuredhighdimensionalgenotypedatawithapplicationstoassortativemating
AT malikosmanasif rbahadurefficientsimulationofstructuredhighdimensionalgenotypedatawithapplicationstoassortativemating

Ejemplares similares