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MendelianRandomization v0.9.0: updates to an R package for performing Mendelian randomization analyses using summarized data
The MendelianRandomization package is a software package written for the R software environment that implements methods for Mendelian randomization based on summarized data. In this manuscript, we describe functions that have been added or edited in the package since version 0.5.0, when we last desc...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
F1000 Research Limited
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10616660/ https://www.ncbi.nlm.nih.gov/pubmed/37915953 http://dx.doi.org/10.12688/wellcomeopenres.19995.2 |
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author | Patel, Ashish Ye, Ting Xue, Haoran Lin, Zhaotong Xu, Siqi Woolf, Benjamin Mason, Amy M. Burgess, Stephen |
author_facet | Patel, Ashish Ye, Ting Xue, Haoran Lin, Zhaotong Xu, Siqi Woolf, Benjamin Mason, Amy M. Burgess, Stephen |
author_sort | Patel, Ashish |
collection | PubMed |
description | The MendelianRandomization package is a software package written for the R software environment that implements methods for Mendelian randomization based on summarized data. In this manuscript, we describe functions that have been added or edited in the package since version 0.5.0, when we last described the package and its contents. The main additions to the package since that time are: 1) new robust methods for performing Mendelian randomization, particularly in the cases of bias from weak instruments and/or winner’s curse, and pleiotropic variants, 2) methods for performing Mendelian randomization with correlated variants using dimension reduction to summarize large numbers of highly correlated variants into a limited set of principal components, 3) functions for calculating first-stage F statistics, representing instrument strength, in both univariable and multivariable contexts, and with uncorrelated and correlated genetic variants. We also discuss some pragmatic issues relating to the use of correlated variants in Mendelian randomization. |
format | Online Article Text |
id | pubmed-10616660 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | F1000 Research Limited |
record_format | MEDLINE/PubMed |
spelling | pubmed-106166602023-11-21 MendelianRandomization v0.9.0: updates to an R package for performing Mendelian randomization analyses using summarized data Patel, Ashish Ye, Ting Xue, Haoran Lin, Zhaotong Xu, Siqi Woolf, Benjamin Mason, Amy M. Burgess, Stephen Wellcome Open Res Software Tool Article The MendelianRandomization package is a software package written for the R software environment that implements methods for Mendelian randomization based on summarized data. In this manuscript, we describe functions that have been added or edited in the package since version 0.5.0, when we last described the package and its contents. The main additions to the package since that time are: 1) new robust methods for performing Mendelian randomization, particularly in the cases of bias from weak instruments and/or winner’s curse, and pleiotropic variants, 2) methods for performing Mendelian randomization with correlated variants using dimension reduction to summarize large numbers of highly correlated variants into a limited set of principal components, 3) functions for calculating first-stage F statistics, representing instrument strength, in both univariable and multivariable contexts, and with uncorrelated and correlated genetic variants. We also discuss some pragmatic issues relating to the use of correlated variants in Mendelian randomization. F1000 Research Limited 2023-11-21 /pmc/articles/PMC10616660/ /pubmed/37915953 http://dx.doi.org/10.12688/wellcomeopenres.19995.2 Text en Copyright: © 2023 Patel A et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Tool Article Patel, Ashish Ye, Ting Xue, Haoran Lin, Zhaotong Xu, Siqi Woolf, Benjamin Mason, Amy M. Burgess, Stephen MendelianRandomization v0.9.0: updates to an R package for performing Mendelian randomization analyses using summarized data |
title | MendelianRandomization v0.9.0: updates to an R package for performing Mendelian randomization analyses using summarized data |
title_full | MendelianRandomization v0.9.0: updates to an R package for performing Mendelian randomization analyses using summarized data |
title_fullStr | MendelianRandomization v0.9.0: updates to an R package for performing Mendelian randomization analyses using summarized data |
title_full_unstemmed | MendelianRandomization v0.9.0: updates to an R package for performing Mendelian randomization analyses using summarized data |
title_short | MendelianRandomization v0.9.0: updates to an R package for performing Mendelian randomization analyses using summarized data |
title_sort | mendelianrandomization v0.9.0: updates to an r package for performing mendelian randomization analyses using summarized data |
topic | Software Tool Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10616660/ https://www.ncbi.nlm.nih.gov/pubmed/37915953 http://dx.doi.org/10.12688/wellcomeopenres.19995.2 |
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