This respoitory holds code and results for our study of age of onset in genetic prion disease:
Minikel EV, Vallabh SM, Orseth MC, Brandel J-P, Haïk S, Laplanche J-L, Zerr I, Parchi P, Capellari S, Safar J, Kenny J, Fong JC, Takada LT, Ponto C, Hermann P, Knipper T, Stehmann C, Kitamoto T, Ae R, Hamaguchi T, Sanjo N, Tsukamoto T, Mizusawa H, Collins SJ, Chiesa R, Roiter I, de Pedro-Cuesta J, Calero M, Geschwind MD, Yamada M, Nakamura Y, Mead S. Age at onset in genetic prion disease and the design of preventive clinical trials. Neurology. 2019 Jun 6; PMID: 31171647. [bioRxiv preprint]
This repository includes the following:
- supplementary materials
- source code (details below)
- figures & tables, including Excel files of the Supplementary Life Tables and Supplementary Duration Tables.
- life tables & other input data
The source code in full_dataset_analysis.R, together with the full, unredacted dataset that is not made public in this repository due to privacy concerns, is necessary to create the life tables as well as Tables S2 and S7, and Figures S2, S4 and S5. Although users cannot reproduce these parts of the analysis, the source code is made public so that you can at least see what we did there.
The source code in public_dataset_analysis.R accepts the life tables as input and is sufficient to reproduce Tables 1, 2, 3, S2, S3, S5, and S6, and Figures 1 and 2, S1, S3, and S6. The simulations are computationally intensive and are not run by default; to re-run these parts of the code, edit TRUE to FALSE in lines such as regenerate_fig_2_data = FALSE.
Tables S1 and S4 are based on literature review and are not derived computationally, thus, these are provided in the manuscript supplement but not anywhere in the source code.
This repository has been archived and given a DOI for permanent access: 10.5281/zenodo.2535761
This work is licensed under a Creative Commons Attribution 4.0 International License.
