About

4-hour video going over these materials

Prerequisites

Have at least a basic knowledge of R,
Install recent versions of R (>= 3.4) and RStudio (>= 1.2),
Install recent versions of {bigstatsr} and {bigsnpr} (e.g. from CRAN),

Download the data used in the tutorials:

runonce::download_file(
  "https://figshare.com/ndownloader/files/38019072",
  dir = "tmp-data", fname = "GWAS_data.zip")  # 109 MB

runonce::download_file(
  "https://figshare.com/ndownloader/files/38019027", 
  dir = "tmp-data", fname = "ref_freqs.csv.gz")  # 46 MB

runonce::download_file(
  "https://figshare.com/ndownloader/files/38019024",
  dir = "tmp-data", fname = "projection.csv.gz")  # 44 MB

runonce::download_file(
  "https://figshare.com/ndownloader/files/38077323",
  dir = "tmp-data", fname = "sumstats_CAD_tuto.csv.gz")  # 16 MB

runonce::download_file(
  "https://figshare.com/ndownloader/files/38247288",
  dir = "tmp-data", fname = "gen_pos_tuto.rds")  # 2.5 MB

bigsnpr::download_plink("tmp-data")   # 6.3 MB
bigsnpr::download_plink2("tmp-data")  # 6.6 MB

#> [1] "tmp-data/GWAS_data.zip"
#> [1] "tmp-data/ref_freqs.csv.gz"
#> [1] "tmp-data/projection.csv.gz"
#> [1] "tmp-data/sumstats_CAD_tuto.csv.gz"
#> [1] "tmp-data/gen_pos_tuto.rds"
#> [1] "tmp-data/plink.exe"
#> [1] "tmp-data/plink2.exe"

License

This material is licensed under the Creative Commons Attribution-ShareAlike 3.0 License.

Author

Florian Privé is a senior researcher in predictive human genetics, fond of Data Science and an R(cpp) enthusiast. You can find him on Twitter and GitHub as @privefl.

Contact

If you want me to add or clarify some content in this documentation, please open an issue on the GitHub repository of this documentation.

If you have bug reports or questions specifically on functions of the packages, please open an issue on the corresponding package’s repository.

I will always redirect you to GitHub issues if you email me about the packages, so that others can benefit from our discussion.

bigsnpr & bigstatsr