Last updated: 2023-07-24
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Knit directory:
SISG2023_Association_Mapping/
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| Rmd | 7a0d62d | Joelle Mbatchou | 2023-07-24 | add practical key session 2 |
| html | 89a89d2 | Joelle Mbatchou | 2023-07-24 | Build site. |
| Rmd | 10c5ea9 | Joelle Mbatchou | 2023-07-24 | add practical key session 1 |
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Instructors: Joelle Mbatchou & Loic Yengo
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 (requires login) – 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:
Please join the module’s Slack channel, where you can ask questions and see real-time updates from the instructors and TAs. Each session builds on previous sessions so you will get maximum benefit by attending every session live and in sequence.
The course schedule is below.
We will use an online server during the module to run exercises (see instructions here for setup). If you decide to run analyses from your local machine instead, follow the instructions below.
Prior to the module, please install working and latest versions of:
All are free software.
Please be sure to install some necessary R packages with:
install.packages("qqman")
install.packages("bigsnpr")
install.packages("hexbin")
install.packages("tidyverse")
install.packages("BEDMatrix")
install.packages("devtools")
install.packages("SKAT")
install.packages("patchwork")
devtools::install_github("yaowuliu/ACAT")
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("GWASTools")All times listed below for the schedule are Pacific Daylight Time (PDT, Seattle time).
| Time | Session | Topic | Lecture | Exercises | Key |
|---|---|---|---|---|---|
| 8:30am-10am | 1 | Introduction, Case Control Association Testing & Association Testing with Quantitative Traits | Intro, Lecture | Exercises | HTML, Rmd |
| 10:30am-12pm | 2 | Introduction to the PLINK Software for GWAS & Population Structure Inference | Lecture | Exercises | HTML, Rmd |
| 1:30pm-3pm | 3 | GWAS in Samples with Structure & Introduction to the REGENIE Software | Lecture | Exercises | |
| 3:30pm-5pm | 4 | Power, Sample Size & Design Considerations | Lecture | Exercises |
| Time | Session | Topic | Lecture | Exercises | Key |
|---|---|---|---|---|---|
| 8:30am-10am | 5 | Downstream analyses: Conditional Analyses, Colocalization, Fine-mapping, Gene-based & Pathways Analysis | Lecture | Exercises | |
| 10:30am-12pm | 6 | Downstream analyses: Polygenic Risk Scores | Lecture | Exercises | |
| 1:30pm-3pm | 7 | Rare Variant Analysis: Collapsing Tests, Kernel (Variance Component) Tests and Omnibus Tests | Lecture | Exercises | |
| 3:30pm-5pm | 8 | Emerging issues showcasing ongoing research | Lecture | Exercises |
| Time | Session | Topic | Lecture | Exercises | Key |
|---|---|---|---|---|---|
| 8:30am-10am | 9 | Beyond traditional GWAS: Variance QTL, Interaction Testing, GWAX, Time-to-event, Multi-trait analysis | Lecture | Exercises | |
| 10:30am-12pm | 10 | Emerging issues showcasing ongoing research | Lecture |
All the data sets used can be downloaded from the Github repository. These have all been loaded on the online server for the class.
sessionInfo()R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4.1
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/Los_Angeles
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