Last updated: 2020-07-23
Checks: 1 1
Knit directory: SlopeHunter/
This reproducible R Markdown analysis was created with workflowr (version 1.6.2). 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 daef612. 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: .Rproj.user/
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 | daef612 | Osama | 2020-07-23 | test ws |
| Rmd | 17c2707 | Osama | 2020-07-23 | Test ws |
| html | 17c2707 | Osama | 2020-07-23 | Test ws |
| Rmd | 85d883b | Osama | 2020-07-23 | Test ws |
| html | 85d883b | Osama | 2020-07-23 | Test ws |
| Rmd | 91edbca | Osama | 2020-07-23 | Test website |
| html | 91edbca | Osama | 2020-07-23 | Test website |
| html | 853776a | Osama | 2020-07-23 | Initial step |
| Rmd | 95f08ec | Osmahmoud | 2020-07-23 | Start workflowr project. |
Slope-Hunter: An approach for collider bias correction in Genome-Wide Association Studies (GWAS) of subsequent traits
This website layout was inspired by the CAUSE website layout.
Here are some useful links:
Studying genetic associations with prognosis (e.g. survival, disability, subsequent disease events) is problematic due to selection bias - also termed index event bias or collider bias - whereby selection on disease status can induce associations between causes of incidence with prognosis.
The ‘Slope-Hunter’ approach is proposed for adjusting genetic associations for this bias. The approach is unbiased even when there is genetic correlation between incidence and prognosis.
Our approach has two stages. First, cluster-based techniques are used to identify: variants affecting neither incidence nor prognosis (these should not suffer bias and only a random sub-sample of them are retained in the analysis); variants affecting prognosis only (excluded from the analysis). Second, we fit a cluster-based model to identify the class of variants only affecting incidence, and use this class to estimate the adjustment factor.