Last updated: 2022-10-06

Checks: 1 1

Knit directory: SlopeHunter/

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: uncommitted changes

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.

Repository version: a81c981

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 a81c981. 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
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    R/.DS_Store

Unstaged changes:
    Modified:   Build_software.R
    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
html a81c981 Osama Mahmoud 2022-10-06 SH website main page updated
Rmd ce85b57 Osama Mahmoud 2022-10-06 Updated workflow and the Github Readme
html 01c13a1 Osama Mahmoud 2022-10-03 Build with No Err/War/Notes
Rmd 61b51b2 Osama 2020-08-20 Update
html 61b51b2 Osama 2020-08-20 Update
Rmd 0201448 Osama 2020-07-24 Update Readme
html 0201448 Osama 2020-07-24 Update Readme
Rmd ac4f0d8 Osama 2020-07-24 R package built
Rmd 8499789 Osama 2020-07-23 Test
html 8499789 Osama 2020-07-23 Test
Rmd bb0225b Osama 2020-07-23 test ws
html bb0225b Osama 2020-07-23 test ws
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.

Welcome to Slope-Hunter website!

Some useful links are as follows:

This website layout was inspired by the layout of the CAUSE website.

1. Introduction to Slope-Hunter

Studying genetic associations with prognosis (e.g., survival, disability, subsequent disease events) or conditional on a phenotype (e.g., disease incidence) may be affected by 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 uses advanced machine learning techniques such as unsupervised model-based clustering tailored to theoretical distributions of genetic effects on incidence and prognosis. The ‘Slope-Hunter’ method identifies and utilises the cluster of genetic variants only affecting incidence to estimate an unbiased adjustment factor for collider bias correction even in the presence genetic correlations (e.g., shared genetic pathways as typically observed for many traits including metabolites, cancer risk factors, psychiatric phenotype). The ‘Slope-Hunter’ approach assumes the identified cluster of variants only affecting incidence explains more variation in incidence than any other variant clusters.

2. What does this website provide?

3. How to cite this work

If you use the ‘Slope-Hunter’ method, please do consider to cite both the paper and the software as follows:

  • Mahmoud, O., Dudbridge, F., Davey Smith, G. et al. A robust method for collider bias correction in conditional genome-wide association studies. Nature Communications 13, 619 (2022). (doi: https://doi.org/10.1038/s41467-022-28119-9).

Note: in the citation below, replace the <X.Y.Z> with the version you have used, and the (20XX) with the year in which that version was released.