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| Rmd | 54deab9 | Joelle Mbatchou | 2025-06-11 | add soln#8 and fix link practical #9 |
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Instructors: Joelle Mbatchou & Michael Epstein
You will find on this website link to lecture slides, exercises including some solutions, and link to the class video recordings.
The official SISG web page can be found here – course evaluations and certificates of completion are available via this page.
The module has 10 sessions, each of 90 minutes. The standard format for a session is approximately:
Each session builds on previous sessions so you will get maximum benefit by attending every session and in sequence.
The course schedule is below.
We will be running exercises during the course using various tools, follow the instructions below to get setup on your machine.
Prior to the module, please install working and latest versions of:
All are free software. For those on Windows, we recommend WSL (Windows Subsystem for Linux) to run the tools above if no Windows binary is available. Alternatively, you can also use docker if docker images are available.
Please be sure to install some necessary R packages by running the following commands in a R terminal:
install.packages("qqman")
install.packages("bigsnpr")
install.packages("hexbin")
install.packages("devtools")
install.packages("tidyverse")
install.packages("cowplot")
install.packages("BEDMatrix")
install.packages("SKAT")
devtools::install_github("yaowuliu/ACAT")All times listed below for the schedule are Eastern Daylight Time (EDT, Atlanta time).
| Time | Session | Topic | Lecture | Exercises | Key |
|---|---|---|---|---|---|
| 8:30am-10am | 1 | Case Control Association Testing & Association Testing with Quantitative Traits | Lecture | Exercises | HTML |
| 10:30am-12pm | 2 | Introduction to the PLINK Software for GWAS & Population Structure Inference | Lecture | Exercises | HTML |
| 1:30pm-3pm | 3 | GWAS in Samples with Structure & Introduction to the REGENIE Software | Lecture | Exercises | HTML |
| 3:30pm-5pm | 4 | Rare Variant Analysis: Collapsing Tests, Kernel (Variance Component) Tests and Omnibus Tests | Lecture | Exercises | HTML |
| Time | Session | Topic | Lecture | Exercises | Key |
|---|---|---|---|---|---|
| 8:30am-10am | 5 | Beyond traditional GWAS: Variance QTL, Interaction Testing, GWAX, Time-to-event, Multi-trait analysis | Lecture | Exercises | HTML |
| 10:30am-12pm | 6 | Downstream analyses: Conditional Analyses, Colocalization, Fine-mapping, Gene-based & Pathways Analysis | Lecture | Exercises | HTML |
| 1:30pm-3pm | 7 | Downstream analyses: Polygenic Risk Scores | Lecture | Exercises | HTML |
| 3:30pm-5pm | 8 | Emerging issues showcasing ongoing research | Lecture |
| Time | Session | Topic | Lecture | Exercises | Key |
|---|---|---|---|---|---|
| 8:30am-10am | 9 | Power, Sample Size & Design Considerations | Lecture | Exercises | HTML |
| 10:30am-12pm | 10 | Emerging issues showcasing ongoing research | Lecture | Exercises |
All the data sets used can be downloaded from the Box folder for the class.
sessionInfo()R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 14.7.4
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_1.1.2
loaded via a namespace (and not attached):
[1] jsonlite_1.8.5 compiler_4.3.0 promises_1.2.0.1 webshot_0.5.5
[5] tidyselect_1.2.0 Rcpp_1.0.10 xml2_1.3.4 stringr_1.5.0
[9] git2r_0.32.0 later_1.3.1 jquerylib_0.1.4 systemfonts_1.0.4
[13] scales_1.2.1 yaml_2.3.7 fastmap_1.1.1 R6_2.5.1
[17] generics_0.1.3 workflowr_1.7.0 knitr_1.43 tibble_3.2.1
[21] kableExtra_1.3.4 munsell_0.5.0 rprojroot_2.0.3 svglite_2.1.1
[25] bslib_0.5.0 pillar_1.9.0 rlang_1.1.1 utf8_1.2.3
[29] cachem_1.0.8 stringi_1.7.12 httpuv_1.6.11 xfun_0.39
[33] fs_1.6.2 sass_0.4.6 viridisLite_0.4.2 cli_3.6.1
[37] magrittr_2.0.3 rvest_1.0.3 digest_0.6.31 rstudioapi_0.14
[41] lifecycle_1.0.3 vctrs_0.6.2 evaluate_0.21 glue_1.6.2
[45] whisker_0.4.1 colorspace_2.1-0 fansi_1.0.4 httr_1.4.6
[49] rmarkdown_2.22 tools_4.3.0 pkgconfig_2.0.3 htmltools_0.5.5