A network algorithm for the X chromosomal exact test for Hardy–Weinberg equilibrium with multiple alleles
Statistical methodology for testing the Hardy-Weinberg equilibrium at X chromosomal variants has recently experienced considerable development. Up to a few years ago, testing X chromosomal variants for equilibrium was basically done by applying autosomal test procedures to females only. At present,...
| Autores: | , |
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| Formato: | artículo |
| Fecha de publicación: | 2021 |
| País: | España |
| Recursos: | Universitat Politècnica de Catalunya (UPC) |
| Repositorio: | UPCommons. Portal del coneixement obert de la UPC |
| Idioma: | inglés |
| OAI Identifier: | oai:upcommons.upc.edu:2117/343817 |
| Acesso em linha: | https://hdl.handle.net/2117/343817 https://dx.doi.org/10.1111/1755-0998.13373 |
| Access Level: | acceso abierto |
| Palavra-chave: | Biomathematics Numerical analysis--Simulation methods Hardy-Weinberg equilibrium Indel Microsatellite Network algorithm Permutation test X chromosome Biomatemàtica Anàlisi numèrica Classificació AMS::92 Biology and other natural sciences::92B Mathematical biology in general Classificació AMS::65 Numerical analysis::65C Probabilistic methods, simulation and stochastic differential equations Àrees temàtiques de la UPC::Matemàtiques i estadística::Matemàtica aplicada a les ciències Àrees temàtiques de la UPC::Matemàtiques i estadística::Anàlisi numèrica |
| Resumo: | Statistical methodology for testing the Hardy-Weinberg equilibrium at X chromosomal variants has recently experienced considerable development. Up to a few years ago, testing X chromosomal variants for equilibrium was basically done by applying autosomal test procedures to females only. At present, male alleles can be taken into account in asymptotic and exact test procedures for both the bi-and multiallelic case. However, current X chromosomal exact procedures for multiple alleles rely on a classical full enumeration algorithm and are computationally expensive, and in practice not feasible for more than three alleles. In this article, we extend the autosomal network algorithm for exact Hardy-Weinberg testing with multiple alleles to the X chromosome, achieving considerable reduction in computation times for multiallelic variants with up to five alleles. The performance of the X chromosomal network algorithm is assessed in a simulation study. Beyond four alleles, a permutation test is, in general, the more feasible approach. A detailed description of the algorithm is given, and examples of X chromosomal indels and microsatellites are discussed. |
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