Last updated: 2021-09-14

Checks: 1 1

Knit directory: proxyMR/

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.

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: 7f198c6

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 7f198c6. 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:    fig_test.RData
    Ignored:    household_MR_exhaustive_summary.rds
    Ignored:    proxyMR_comparison.RData
    Ignored:    proxyMR_figure_data.RData
    Ignored:    renv/library/
    Ignored:    renv/local/
    Ignored:    renv/staging/
    Ignored:    traits_corr2_update.rds

Untracked files:
    Untracked:  R/proxyMR_figures.R
    Untracked:  R/proxyMR_hiercharchy.R

Unstaged changes:
    Modified:   analysis/about.Rmd
    Modified:   analysis/index.Rmd
    Modified:   analysis/update_meeting_06_09_2021.Rmd
    Modified:   analysis/update_meeting_14_06_2021.Rmd
    Modified:   analysis/update_meeting_14_07_2021.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	557181f	jennysjaarda	2021-08-31	clean up more website docs
Rmd	b849be4	jennysjaarda	2021-08-31	clean up some website docs
html	b849be4	jennysjaarda	2021-08-31	clean up some website docs
html	a55da5b	jennysjaarda	2021-07-22	Build site.
Rmd	b0b81d9	jennysjaarda	2021-07-22	Updating website
html	021aeb8	jennysjaarda	2021-06-18	Build site.
html	b02d111	jennysjaarda	2021-06-18	Build site.
Rmd	e1aeb5f	jennysjaarda	2021-06-02	Start workflowr project.

This is the website for the research project “proxyMR”.

If you have cloned the project to a local computer this website is rendered in the docs subdirectory of the project directory.

If you are using workflowr to publish the research website it will also be rendered online to GitHub Pages.

This page acts as a table of contents for the website. There are links to the web pages generated from the analysis notebooks and to the rendered versions of manuscripts/documents/presentations.

Overview documents

About

This notebook explains the central ideas behind the project.

Notes

This notebook is for keeping notes of any points that may be useful for later project or manuscript development.

To do

Current tasks and completed tasks (roughly organized by dates/weeks).

Workflow management

This project uses the targets and workflowr packages for managing the workflow of the project (making sure that the dependencies between computational steps are satisfied). This notebook contains notes on the proposed workflow for using targets and workflowr.

Meetings

Weekly meeting were held roughly once per week or every other week.

Publications and Presentations

Group Meeting 07-09-2021

Analyses Notebooks

These notebooks capture the analyses that were carried out to develop the code of the core processing pipeline.

1. Prepare data

Prepare phenotypes and couples for analysis in MR pipeline.

2. Run MR pipeline

MR between partners (partner vs index)

Identify SNP-exposure effects (GW-significance) for phenotypes (sex specific) from Neale database [\(X_{i} \sim G_{i}\)].
Test SNP-outcome effects between genetic instruments and partner outcome phenotypes (sex specific) [\(Y_{p} \sim G_{i}\)].
Combine in MR to assess causal relationships between index and partner [\(Y_{p} \sim X_{i}\)].

Assortative mating MR

Restrict to only MRs where exposure is the same as outcome (for downstream analyses) [\(X_{p} \sim X_{i}\)].

MR within same individual

Identify SNP-exposure effects (GW-significance) for phenotypes (sex specific) from Neale database [\(X_{i} \sim G_{i}\)].
Pull SNP-outcome effects between genetic instruments and outcome phenotypes (sex specific) from Neale database [\(Y_{i} \sim G_{i}\)].
Combine in MR to assess causal relationship between all phenotypes [\(Y_{i} \sim X_{i}\)].

Compare paths towards outcome in partner

Compare paths from index exposure phenotype to partner outcome phenotype [\(X_{i} \rightarrow Y_{p}\)].

PC correlation among couples

Acknowledgements

Primary analysis performed by: Jenny Sjaarda.

Project supervisor: Professor Zoltan Kutalik.

This work has been supported by the Swiss National Science Foundation.

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