Last updated: 2023-08-15
Checks: 1 1
Knit directory: natarajanlab_wiki/
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.
The R Markdown file has unstaged changes. To know which version of
the R Markdown file created these results, you’ll want to first commit
it to the Git repo. If you’re still working on the analysis, you can
ignore this warning. When you’re finished, you can run
wflow_publish to commit the R Markdown file and build the
HTML.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.
The results in this page were generated with repository version c2c5e3c. 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:
Ignored files:
Ignored: .DS_Store
Untracked files:
Untracked: analysis/ldpred.Rmd
Unstaged changes:
Modified: analysis/index.Rmd
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the repository in which changes were
made to the R Markdown (analysis/index.Rmd) and HTML
(docs/index.html) files. If you’ve configured a remote Git
repository (see ?wflow_git_remote), click on the hyperlinks
in the table below to view the files as they were in that past version.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 39f3401 | Your Name | 2023-04-30 | Update |
| Rmd | bbe1af3 | Your Name | 2021-12-16 | Updated |
| html | bbe1af3 | Your Name | 2021-12-16 | Updated |
| html | c035bde | Your Name | 2021-05-14 | Build site. |
| Rmd | 7f29896 | Your Name | 2021-05-14 | wflow_publish("~/natarajanlab_wiki/analysis/index.Rmd") |
| html | bfc3053 | Your Name | 2021-05-14 | Build site. |
| html | 805c7a5 | Your Name | 2021-05-14 | Build site. |
| Rmd | bd58935 | Your Name | 2021-05-14 | wflow_publish("~/natarajanlab_wiki/analysis/index.Rmd") |
| html | c6a3bd7 | Your Name | 2021-05-14 | Build site. |
| Rmd | 8559960 | Your Name | 2021-05-14 | wflow_publish("~/natarajanlab_wiki/analysis/index.Rmd") |
| html | 7675964 | Your Name | 2021-05-14 | Build site. |
| Rmd | 9a1617b | Your Name | 2021-05-14 | wflow_git_commit("analysis/index.Rmd") |
| html | b053d72 | Your Name | 2021-05-14 | Build site. |
| Rmd | a1e1336 | Your Name | 2021-05-14 | wflow_publish("analysis/*.Rmd") |
| Rmd | f8dbdc0 | Your Name | 2021-05-13 | Update |
| html | f8dbdc0 | Your Name | 2021-05-13 | Update |
| html | 284c5f6 | Your Name | 2021-05-13 | Build site. |
| html | 4af313a | Your Name | 2021-05-13 | Build site. |
| Rmd | d02ebab | Your Name | 2021-05-13 | Update |
| html | d02ebab | Your Name | 2021-05-13 | Update |
| Rmd | 8b1b38e | Your Name | 2021-05-13 | Update |
| html | 8b1b38e | Your Name | 2021-05-13 | Update |
| html | 5f41864 | Your Name | 2021-05-12 | update |
| html | decca40 | Your Name | 2021-05-12 | Build site. |
| Rmd | cebfba5 | Your Name | 2021-05-12 | wflow_publish("analysis/index.rmd") |
| Rmd | 47f4912 | Your Name | 2021-05-12 | Update |
| html | 47f4912 | Your Name | 2021-05-12 | Update |
| Rmd | 3f30c15 | Your Name | 2021-05-12 | Update |
| html | 3f30c15 | Your Name | 2021-05-12 | Update |
| html | cd28e0b | Your Name | 2021-05-12 | Build site. |
| Rmd | 41905fe | Your Name | 2021-05-12 | wflow_publish("~/natarajanlab_wiki/analysis/index.Rmd") |
| html | 2a5abe9 | Sarah Urbut | 2021-05-12 | Build site. |
| html | e3d552a | Sarah Urbut | 2021-05-12 | Build site. |
| Rmd | d3cac8d | Sarah Urbut | 2021-05-12 | wflow_publish("analysis/index.Rmd") |
| html | 3615948 | Sarah Urbut | 2021-05-12 | Build site. |
| Rmd | 27ea1b4 | Sarah Urbut | 2021-05-12 | Start workflowr project. |
Welcome! This is a repo to share the code that other members of the lab are working on. We can continuously update it with codes that we refer to often, questions we ask, or resources we find helpful. If you have a script you think might be useful to have on the site, please let me know via github or email and will push!
Click here for the code to LDscore omnigenic plots
Click here for the code to ash_mash_comparison
Click here for the code to torus_metaplot
Click here to see the results of the mash fit on lipids for the top covariance matrices
Click here for the code to Venn Diagrams comparing UKB and MVP output and reproduction with mash, mtag and univariate ash
Click here for sample code to compute the LDpred2 scores with mash summary inputs using SOS.
Click here for sample code to compute the LDpred2 scores with mash summary inputs using R and plink.
And here are some useful scripts for coding in the lab:
Click here for the code to PoPs
Click here for the code to selecting by 500 kb blocks
Click here for sample code to run PRS-CS
Click here for sample code to run PRS-CT
I love these 5 Minute Stats lessons to illustrate key concepts.
For a tutorial on how to run mashR I like the eQTL vignette within this intro, and you can find other informative updates here as well.