Last updated: 2022-05-30

Checks: 7 0

Knit directory: SISG2022_Association_Mapping/

This reproducible R Markdown analysis was created with workflowr (version 1.7.0). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

R Markdown file: up-to-date

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Environment: empty

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Seed: set.seed(20220530)

The command set.seed(20220530) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.

Session information: recorded

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Repository version: 0f3e6d6

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The results in this page were generated with repository version 0f3e6d6. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated: 


working directory clean

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File Version Author Date Message
Rmd f334c30 Joelle Mbatchou 2022-05-30 wflow_git_commit("analysis/index.Rmd")
html 16d00cd Joelle Mbatchou 2022-05-30 Build site.
Rmd cff096b Joelle Mbatchou 2022-05-30 wflow_git_commit("analysis/index.Rmd")
html e5c9bc9 Joelle Mbatchou 2022-05-30 Build site.
Rmd 59bb3ad Joelle Mbatchou 2022-05-30 wflow_git_commit("analysis/index.Rmd")
html 3082268 Joelle Mbatchou 2022-05-30 Build site.
Rmd 796cc41 Joelle Mbatchou 2022-05-30 wflow_git_commit("analysis/index.Rmd")
html e4cde44 Joelle Mbatchou 2022-05-30 Build site.
Rmd a967ab4 Joelle Mbatchou 2022-05-30 wflow_git_commit("analysis/index.Rmd")
html d0c1d42 Joelle Mbatchou 2022-05-30 Build site.
Rmd 7b68d3b Joelle Mbatchou 2022-05-30 wflow_git_commit("analysis/index.Rmd")
html 2f9b400 Joelle Mbatchou 2022-05-30 Build site.
Rmd c7ce0e7 Joelle Mbatchou 2022-05-30 wflow_git_commit("analysis/index.Rmd")
html cef4758 Joelle Mbatchou 2022-05-30 Build site.
Rmd 765947b Joelle Mbatchou 2022-05-30 wflow_git_commit("analysis/index.Rmd")
html 069ecca Joelle Mbatchou 2022-05-30 Build site.
Rmd 119de75 Joelle Mbatchou 2022-05-30 wflow_git_commit("analysis/index.Rmd")
html ade7902 Joelle Mbatchou 2022-05-30 Build site.
Rmd 2fe4987 Joelle Mbatchou 2022-05-30 wflow_git_commit("analysis/index.Rmd")
html 4f063b5 Joelle Mbatchou 2022-05-30 Build site.
Rmd 215d78c Joelle Mbatchou 2022-05-30 wflow_git_commit("analysis/index.Rmd")
html 7f88fe6 Joelle Mbatchou 2022-05-30 Build site.
Rmd f8c0f87 Joelle Mbatchou 2022-05-30 wflow_git_commit("analysis/index.Rmd")
html 6be8fe2 Joelle Mbatchou 2022-05-30 Build site.
html c1f9d96 Joelle Mbatchou 2022-05-30 Build site.
Rmd 17f78ac Joelle Mbatchou 2022-05-30 wflow_git_commit("analysis/index.Rmd")
html eed64d3 Joelle Mbatchou 2022-05-30 Build site.
Rmd 0f9d8aa Joelle Mbatchou 2022-05-30 wflow_git_commit("analysis/index.Rmd")
html 058b096 Joelle Mbatchou 2022-05-30 Build site.
Rmd 18141b0 Joelle Mbatchou 2022-05-30 wflow_git_commit("analysis/index.Rmd")
html ba7e38b Joelle Mbatchou 2022-05-30 Build site.
Rmd d71c883 Joelle Mbatchou 2022-05-30 wflow_git_commit("analysis/index.Rmd")
html ed2a0a7 Joelle Mbatchou 2022-05-30 Build site.
Rmd 084f0e3 Joelle Mbatchou 2022-05-30 modify site
Rmd 4e98bda Joelle Mbatchou 2022-05-30 modify index page
Rmd 5bd3258 Joelle Mbatchou 2022-05-30 wflow_git_commit(all = TRUE)
Rmd 75bd646 Joelle Mbatchou 2022-05-30 Start workflowr project.

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:

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 tentative course schedule is below.

Pre-requisites

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("ggplot2")

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