Last updated: 2020-12-04
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Knit directory: popstruct_scripts/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 99813ec | Arslan-Zaidi | 2020-12-03 | organizing workflowr project |
| html | 99813ec | Arslan-Zaidi | 2020-12-03 | organizing workflowr project |
| Rmd | 31a95ef | Arslan Zaidi | 2020-11-23 | Start workflowr project. |
This repository contains scripts and code to carry out the analyses in:
Demographic history impacts stratification in polygenic scores Arslan A. Zaidi, Iain Mathieson
bioRxiv 2020.07.20.212530 doi: https://doi.org/10.1101/2020.07.20.212530
Please cite this paper if you use any of the code in your own analyses.
The following is a brief description of each folder. The wiki page contains additional information on how scripts were chained etc. for each analysis.
/optimize_migration_rate : scripts used to choose migration rate between demes such that the Fst and genomic inflation (on birthplace) matches that observed in the UK Biobank.
/simulating_genotypes : scripts to carry out msprime simulations, output the genotypes from these simulations, and run PCA on those genotypes. The folder is organized further by different demographic models used: - /grid : Simulations carried out for individuals sampled in a 6x6 square grid. - tau-9 : Individuals sampled in a 6x6 grid where all demes remain structured back in time (i.e. perpetual model) - tau100 : Individuals sampled in a 6x6 grid where all demes become panmictic 100 generations in the past. - /ukb : Simulations carried out for individuals sampled from 35 demes arranged according to the geographic structure in England and Wales.
/pca_plots : scripts used to generate scatter plots of eigenvectors from PCA carried out on simulated genotype data
/gwas : scripts used to simulate phenotypes, carry out GWAS, and construct polygenic scores.
/burden_msprime: scripts used to carry out burden tests