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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.
Affiliation
  • Packer RJ; Department of Population Health Sciences, University of Leicester, Leicester LE1 7RH, UK.
  • Williams AT; Leicester National Institute of Health and Care Research Biomedical Research Centre, Glenfield Hospital, Leicester LE5 4PW, UK.
  • Hennah W; Department of Population Health Sciences, University of Leicester, Leicester LE1 7RH, UK.
  • Eisenberg MT; Orion Pharma, Espoo 02200, Finland.
  • Shrine N; Neuroscience Center, HiLIFE, University of Helsinki, Helsinki 00100, Finland.
  • Fawcett KA; Institute for Molecular Medicine FIMM, HiLIFE, University of Helsinki, Helsinki 00100, Finland.
  • Pearson W; Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK.
  • Guyatt AL; Department of Population Health Sciences, University of Leicester, Leicester LE1 7RH, UK.
  • Edris A; Department of Population Health Sciences, University of Leicester, Leicester LE1 7RH, UK.
  • Hollox EJ; Department of Population Health Sciences, University of Leicester, Leicester LE1 7RH, UK.
  • Marttila M; Department of Population Health Sciences, University of Leicester, Leicester LE1 7RH, UK.
  • Rao BS; Department of Population Health Sciences, University of Leicester, Leicester LE1 7RH, UK.
  • Bratty JR; Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, Gent 9000, Belgium.
  • Wain LV; Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK.
  • Dudbridge F; Orion Pharma, Espoo 02200, Finland.
  • Tobin MD; Orion Pharma, Nottingham NG1 2GB, UK.
Bioinformatics ; 39(4)2023 04 03.
Article in En | MEDLINE | ID: mdl-36744935
ABSTRACT

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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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Software / Phenomics Type of study: Risk_factors_studies Language: En Journal: Bioinformatics Year: 2023 Document type: Article
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PubMed Links
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Software / Phenomics Type of study: Risk_factors_studies Language: En Journal: Bioinformatics Year: 2023 Document type: Article