Last updated: 2022-05-30

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Knit directory: SISG2022_Association_Mapping/

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Welcome to the website for the Summer Institue in Statistical Genetics module: Association mapping and Sequencing.

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.

Session Format

The module has 10 sessions, each of 80 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 Please join the module’s Slack channel, where you can ask questions and see real-time updates from the instructors and TAs.

We will cover a total of 8 sessions split between July 25-27th. The tentative course schedule is below. Material will be delivered via zoom by live lectures and live practical sessions, with additional reading materials and/or slides also provided. Each session builds on previous sessions so you will get maximum benefit by attending every session live and in sequence.

Pre-requisites

Prior to the module, please install working versions of:

All are free software. REGENIE requires MAC/Linux system; if you have a Windows laptop, you can install docker to setup a Linux image (see here).

Please be sure to install some necessary R packages with

install.packages("qqman")

Schedule

This is a tentative schedule. All times listed below for the schedule are Pacific Standard Time (Seattle time, PST).

Datasets

All individual data files below can be downloaded from two zipped folder from dropbox:

Alternatively, you can download each of the data files in the Github repository.


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] workflowr_1.7.0

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.8.3     rstudioapi_0.13  knitr_1.31       whisker_0.4     
 [5] magrittr_1.5     getPass_0.2-2    R6_2.4.1         rlang_1.0.1     
 [9] fastmap_1.1.0    stringr_1.4.0    httr_1.4.3       tools_3.6.1     
[13] xfun_0.31        cli_3.1.1        jquerylib_0.1.4  git2r_0.30.1    
[17] htmltools_0.5.2  yaml_2.2.1       digest_0.6.25    rprojroot_2.0.3 
[21] tibble_2.1.3     crayon_1.3.4     processx_3.5.3   callr_3.7.0     
[25] later_1.3.0      sass_0.4.0       promises_1.2.0.1 fs_1.5.2        
[29] ps_1.7.0         glue_1.6.1       evaluate_0.14    rmarkdown_2.14  
[33] stringi_1.4.6    bslib_0.3.1      pillar_1.4.3     compiler_3.6.1  
[37] jsonlite_1.7.2   httpuv_1.6.5     pkgconfig_2.0.3