Optimal linkage disequilibrium splitting

MOTIVATION: A few algorithms have been developed for splitting the genome in nearly independent blocks of linkage disequilibrium. Due to the complexity of this problem, these algorithms rely on heuristics, which makes them suboptimal. RESULTS: Here, we develop an optimal solution for this problem us...

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Detalles Bibliográficos
Autor principal: Privé, Florian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2021
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8696101/
https://www.ncbi.nlm.nih.gov/pubmed/34260708
http://dx.doi.org/10.1093/bioinformatics/btab519
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author Privé, Florian
author_facet Privé, Florian
author_sort Privé, Florian
collection PubMed
description MOTIVATION: A few algorithms have been developed for splitting the genome in nearly independent blocks of linkage disequilibrium. Due to the complexity of this problem, these algorithms rely on heuristics, which makes them suboptimal. RESULTS: Here, we develop an optimal solution for this problem using dynamic programming. AVAILABILITY: This is now implemented as function snp_ldsplit as part of R package bigsnpr. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-86961012022-01-04 Optimal linkage disequilibrium splitting Privé, Florian Bioinformatics Applications Notes MOTIVATION: A few algorithms have been developed for splitting the genome in nearly independent blocks of linkage disequilibrium. Due to the complexity of this problem, these algorithms rely on heuristics, which makes them suboptimal. RESULTS: Here, we develop an optimal solution for this problem using dynamic programming. AVAILABILITY: This is now implemented as function snp_ldsplit as part of R package bigsnpr. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2021-07-14 /pmc/articles/PMC8696101/ /pubmed/34260708 http://dx.doi.org/10.1093/bioinformatics/btab519 Text en © The Author(s) 2021. 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 Notes
Privé, Florian
Optimal linkage disequilibrium splitting
title Optimal linkage disequilibrium splitting
title_full Optimal linkage disequilibrium splitting
title_fullStr Optimal linkage disequilibrium splitting
title_full_unstemmed Optimal linkage disequilibrium splitting
title_short Optimal linkage disequilibrium splitting
title_sort optimal linkage disequilibrium splitting
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8696101/
https://www.ncbi.nlm.nih.gov/pubmed/34260708
http://dx.doi.org/10.1093/bioinformatics/btab519
work_keys_str_mv AT priveflorian optimallinkagedisequilibriumsplitting

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