DeepPheWAS: an R package for phenotype generation and association analysis for phenome-wide association studies

SUMMARY: DeepPheWAS is an R package for phenome-wide association studies that creates clinically curated composite phenotypes and integrates quantitative phenotypes from primary care data, longitudinal trajectories of quantitative measures, disease progression and drug response phenotypes. Tools are...

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Autores principales: Packer, Richard J, Williams, Alex T, Hennah, William, Eisenberg, Micaela T, Shrine, Nick, Fawcett, Katherine A, Pearson, Willow, Guyatt, Anna L, Edris, Ahmed, Hollox, Edward J, Marttila, Mikko, Rao, Balasubramanya S, Bratty, John Raymond, Wain, Louise V, Dudbridge, Frank, Tobin, Martin D
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
Materias:
Applications Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10070035/
https://www.ncbi.nlm.nih.gov/pubmed/36744935
http://dx.doi.org/10.1093/bioinformatics/btad073
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author Packer, Richard J
Williams, Alex T
Hennah, William
Eisenberg, Micaela T
Shrine, Nick
Fawcett, Katherine A
Pearson, Willow
Guyatt, Anna L
Edris, Ahmed
Hollox, Edward J
Marttila, Mikko
Rao, Balasubramanya S
Bratty, John Raymond
Wain, Louise V
Dudbridge, Frank
Tobin, Martin D
author_facet Packer, Richard J
Williams, Alex T
Hennah, William
Eisenberg, Micaela T
Shrine, Nick
Fawcett, Katherine A
Pearson, Willow
Guyatt, Anna L
Edris, Ahmed
Hollox, Edward J
Marttila, Mikko
Rao, Balasubramanya S
Bratty, John Raymond
Wain, Louise V
Dudbridge, Frank
Tobin, Martin D
author_sort Packer, Richard J
collection PubMed
description SUMMARY: DeepPheWAS is an R package for phenome-wide association studies that creates clinically curated composite phenotypes and integrates quantitative phenotypes from primary care data, longitudinal trajectories of quantitative measures, disease progression and drug response phenotypes. Tools are provided for efficient analysis of association with any genetic input, under any genetic model, with optional sex-stratified analysis, and for developing novel phenotypes. AVAILABILITY AND IMPLEMENTATION: The DeepPheWAS R package is freely available under GNU general public licence v3.0 from at https://github.com/Richard-Packer/DeepPheWAS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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spelling pubmed-100700352023-04-04 DeepPheWAS: an R package for phenotype generation and association analysis for phenome-wide association studies Packer, Richard J Williams, Alex T Hennah, William Eisenberg, Micaela T Shrine, Nick Fawcett, Katherine A Pearson, Willow Guyatt, Anna L Edris, Ahmed Hollox, Edward J Marttila, Mikko Rao, Balasubramanya S Bratty, John Raymond Wain, Louise V Dudbridge, Frank Tobin, Martin D Bioinformatics Applications Note SUMMARY: DeepPheWAS is an R package for phenome-wide association studies that creates clinically curated composite phenotypes and integrates quantitative phenotypes from primary care data, longitudinal trajectories of quantitative measures, disease progression and drug response phenotypes. Tools are provided for efficient analysis of association with any genetic input, under any genetic model, with optional sex-stratified analysis, and for developing novel phenotypes. AVAILABILITY AND IMPLEMENTATION: The DeepPheWAS R package is freely available under GNU general public licence v3.0 from at https://github.com/Richard-Packer/DeepPheWAS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. Oxford University Press 2023-02-06 /pmc/articles/PMC10070035/ /pubmed/36744935 http://dx.doi.org/10.1093/bioinformatics/btad073 Text en © The Author(s) 2023. 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 Note
Packer, Richard J
Williams, Alex T
Hennah, William
Eisenberg, Micaela T
Shrine, Nick
Fawcett, Katherine A
Pearson, Willow
Guyatt, Anna L
Edris, Ahmed
Hollox, Edward J
Marttila, Mikko
Rao, Balasubramanya S
Bratty, John Raymond
Wain, Louise V
Dudbridge, Frank
Tobin, Martin D
DeepPheWAS: an R package for phenotype generation and association analysis for phenome-wide association studies
title DeepPheWAS: an R package for phenotype generation and association analysis for phenome-wide association studies
title_full DeepPheWAS: an R package for phenotype generation and association analysis for phenome-wide association studies
title_fullStr DeepPheWAS: an R package for phenotype generation and association analysis for phenome-wide association studies
title_full_unstemmed DeepPheWAS: an R package for phenotype generation and association analysis for phenome-wide association studies
title_short DeepPheWAS: an R package for phenotype generation and association analysis for phenome-wide association studies
title_sort deepphewas: an r package for phenotype generation and association analysis for phenome-wide association studies
topic Applications Note
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10070035/
https://www.ncbi.nlm.nih.gov/pubmed/36744935
http://dx.doi.org/10.1093/bioinformatics/btad073
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