Last updated: 2024-06-05

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Knit directory: SISG2024_Association_Mapping/

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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.

Session Format

The module has 10 sessions, each of 90 minutes. The standard format for a session is approximately:

  • 45 minutes of lecture material that will be recorded via Zoom live and posted at the end of the day
  • 30 minutes of exercises for you to try, with small-group “breakout” Zoom sessions available, attended by other class participants, and Teaching Assistants
  • 15 minute discussion of exercises, where the instructors will present possible solutions and answer questions

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.

Pre-requisites

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.

Please be sure to install some necessary R packages with:

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")

Schedule

All times listed below for the schedule are Eastern Daylight Time (EDT, Atlanta time).

Wednesday, June 12th
Time Session Topic Lecture Exercises Key
1:30pm-3pm 1 Introduction, Case Control Association Testing & Association Testing with Quantitative Traits [Intro], [Lecture] Exercises [HTML], [Rmd]
3:30pm-5pm 2 Introduction to the PLINK Software for GWAS & Population Structure Inference [Lecture] Exercises [HTML], [Rmd]
Thursday, June 13th
Time Session Topic Lecture Exercises Key
8:30am-10am 3 GWAS in Samples with Structure & Introduction to the REGENIE Software [Lecture] Exercises [HTML], [Rmd]
10:30am-12pm 4 Power, Sample Size & Design Considerations [Lecture] Exercises [HTML], [Rmd]
1:30pm-3pm 5 Downstream analyses: Conditional Analyses, Colocalization, Fine-mapping, Gene-based & Pathways Analysis [Lecture] Exercises [HTML], [Rmd]
3:30pm-5pm 6 Downstream analyses: Polygenic Risk Scores [Lecture] Exercises [HTML], [Rmd]
Friday, June 14th
Time Session Topic Lecture Exercises Key
8:30am-10am 7 Rare Variant Analysis: Collapsing Tests, Kernel (Variance Component) Tests and Omnibus Tests [Lecture] Exercises [HTML], [Rmd]
10:30am-12pm 8 Emerging issues showcasing ongoing research Lecture Exercises [HTML], [Rmd]
1:30pm-3pm 9 Beyond traditional GWAS: Variance QTL, Interaction Testing, GWAX, Time-to-event, Multi-trait analysis [Lecture] Exercises
3:30pm-5pm 10 Emerging issues showcasing ongoing research Lecture

Datasets

All the data sets used can be downloaded from the Box folder for the class.

Additional resources


sessionInfo()
R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 14.5

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/Chicago
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