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SISG2022_Association_Mapping/
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Instructors: Loic Yengo & Joelle Mbatchou
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.
Prior to the module, please install working and latest versions of:
All are free software. REGENIE requires MAC/Linux system; if you have a Windows laptop, you can use docker to setup a Linux image (see guide here).
Please be sure to install some necessary R packages with:
install.packages("qqman")
install.packages("GWASTools")
install.packages("bigsnpr")
install.packages("dplyr")
install.packages("tidyr")
install.packages("ggplot2")All times listed below for the schedule are Pacific Standard Time (PST, Seattle time).
| Time | Session | Topic | Lecture | Exercises | Key |
|---|---|---|---|---|---|
| 8:00am-9:30am | 1 | Introduction, Case Control Association Testing & Association Testing with Quantitative Traits | Intro, Lecture, Video | Exercises, Video | [.html ], [.Rmd] |
| 10am-11:30am | 2 | Introduction to the PLINK Software for GWAS & Population Structure Inference | Lecture, Video | Exercises, Video | [.html ], [.Rmd] |
| 12pm-1:30pm | 3 | GWAS in Samples with Structure & Introduction to the REGENIE Software | Lecture, Video | Exercises, Video | [.html ], [.Rmd] |
| 1:45pm-2:30pm | 4 | Power, Sample Size & Design Considerations | Lecture, Video | Exercises, Video | [.html ], [.Rmd] |
| Time | Session | Topic | Lecture | Exercises | Key |
|---|---|---|---|---|---|
| 8:00am-9:30am | 5 | Downstream analyses: conditional analyses, colocalization & fine-mapping | Intro, Lecture, Video | Exercises, Video | [.html ], [.Rmd] |
| 10am-11:30am | 6 | Downstream analyses: gene-based and pathways analysis & polygenic risk scores | Lecture, Video | Exercises, Video | [.html ], [.Rmd] |
| 12pm-1:30pm | 7 | Rare Variant Analysis: Collapsing Tests, Kernel (Variance Component) Tests and Omnibus Tests | Lecture, Video | Exercises, Video | [.html ], [.Rmd] |
| 1:45pm-2:30pm | 8 | Emerging issues showcasing ongoing research | Lecture, Video | Exercises, Video | [.html ], [.Rmd] |
| Time | Session | Topic | Lecture | Exercises | Key |
|---|---|---|---|---|---|
| 8:00am-9:30am | 9 | Beyond traditional GWAS: Variance QTL, Interaction Testing, GWAX, Time-to-event, Multi-trait analysis | Intro, Lecture, Video | Exercises, Video | [.html ], [.Rmd] |
| 10am-11am | 10 | Emerging Issues showcasing ongoing research | Lecture, Video | Exercises, Video | [.html ], [.Rmd] |
All individual data files below can be downloaded from a zipped folder in Dropbox.
Alternatively, you can download the files from the Github repository (the largest file “Transferrin.bed” can be downloaded from the Dropbox folder above).
sessionInfo()R version 3.6.1 (2019-07-05)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_1.0.8 workflowr_1.7.0
loaded via a namespace (and not attached):
[1] tidyselect_1.1.1 xfun_0.31 bslib_0.3.1 purrr_0.3.3
[5] colorspace_2.0-0 vctrs_0.3.8 generics_0.0.2 htmltools_0.5.2
[9] viridisLite_0.3.0 yaml_2.2.1 utf8_1.1.4 rlang_1.0.1
[13] later_1.3.0 pillar_1.7.0 jquerylib_0.1.4 glue_1.6.1
[17] lifecycle_1.0.1 stringr_1.4.0 munsell_0.5.0 rvest_1.0.2
[21] kableExtra_1.3.4 evaluate_0.14 knitr_1.31 callr_3.7.0
[25] fastmap_1.1.0 httpuv_1.6.5 ps_1.7.0 fansi_0.4.1
[29] Rcpp_1.0.8.3 promises_1.2.0.1 scales_1.1.1 webshot_0.5.3
[33] jsonlite_1.7.2 fs_1.5.2 systemfonts_1.0.2 digest_0.6.25
[37] stringi_1.4.6 processx_3.5.3 getPass_0.2-2 rprojroot_2.0.3
[41] cli_3.1.1 tools_3.6.1 magrittr_1.5 sass_0.4.0
[45] tibble_2.1.3 crayon_1.3.4 whisker_0.4 pkgconfig_2.0.3
[49] ellipsis_0.3.2 xml2_1.3.3 rmarkdown_2.14 svglite_2.1.0
[53] httr_1.4.3 rstudioapi_0.13 R6_2.4.1 git2r_0.30.1
[57] compiler_3.6.1