Chapter 1 Course information

1.1 Prerequisites

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

Create an RStudio project for this course and download the data to be 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"

1.2 Schedule of SMARTbiomed Summer school

Time	Activity
Monday 13:00–16:30	Starting part 1 (chapters 2 to 5)
Tuesday 09:00–12:00 and 13:00–16:00	Continuing part 1
Wednesday 09:00–10:00	Finishing part 1 + general Q&A
Wednesday 10:30–12:00 and 13:00–15:30	Language exchange workshop (with everyone)
Wednesday 16:00–17:00	Starting part 2 (chapters 6 to 10)
Thursday 09:00–12:00 and 13:00–16:30	Continuing part 2
Friday 09:00–12:00	Finishing part 2 + general Q&A

1.3 Main author

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

1.4 Contact

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

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. Search through existing issues; your question might have already been asked and answered.

1.5 License

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

Statistical Human Genetics course using R