Last updated: 2022-03-07

Checks: 2 0

Knit directory: proxyMR/

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R Markdown file: up-to-date

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Repository version: 81074c1

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The results in this page were generated with repository version 81074c1. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

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Ignored files:
    Ignored:    .DS_Store
    Ignored:    .Rhistory
    Ignored:    .Rproj.user/
    Ignored:    proxyMR_figure_data.RData
    Ignored:    renv/library/
    Ignored:    renv/local/
    Ignored:    renv/staging/

Untracked files:
    Untracked:  R/proxyMR_figures.R
    Untracked:  R/proxyMR_hiercharchy.R
    Untracked:  analysis/project_status.Rmd

Unstaged changes:
    Modified:   R/functions.R
    Modified:   _targets.R
    Modified:   analysis/phenotype_selection.Rmd
    Modified:   analysis/update_meeting_15_10_2021.Rmd

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/todo_list.Rmd) and HTML (docs/todo_list.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 81074c1 jennysjaarda 2022-03-07 wflow_publish(“analysis/todo_list.Rmd”)
Rmd 1afb033 jennysjaarda 2021-09-14 add some documents to the website
html 1afb033 jennysjaarda 2021-09-14 add some documents to the website
html 7f198c6 Jenny Sjaarda 2021-09-14 Build site.
Rmd f8ee7b4 jennysjaarda 2021-09-14 add a few Rmd notebooks

1 06/09/2021

  • Sum \(\rho\) and \(\gamma\).
  • Meta-analyzed binned results across sexes.
  • Fix variance calculation mistake in calculating \(\rho\) and \(\gamma\).
  • Write script/function which replaces Neale_ID with trait description.
  • Clean up index.Rmd
  • Clean up about.Rmd
  • Add Rmd building to targets pipeline.
  • MVMR.
  • AM MR summary Rmd (and publish).
  • PC correlation among couples summary Rmd.
  • Clean up update meeting Rmd.
    • 14-06-21
    • 05-07-21
    • 14-07-21
    • 25-08-21
    • 06-09-21
  • Delete latex_test docs.

2 08/09/2021

  • Weight trend line by inverse variance.
  • Update AF in Neale summary stats.
  • Create couple selection Rmd.
  • Number of tests for filtering by \(\omega\) should exclude those with only one trait. (i.e. number of tests would be \(j^2 - j\)).
  • Filter by \(\omega\) instead of same-person MR.
  • Force intercept through 0 in omega vs gamma/rho plot.
  • Explore impact of meta-anlaysis at SNP/trait level vs. MR-level.
    • Meta-analyze standard MR SNP/trait estimates across sexes.
  • Hierarchy figure (add labels).
  • Make visio figures in LucidChart.
  • Explore IV overlap between X and Y:
    • Determine percentage of IV overlap between X IVs and Y IVs.
    • MV MR, add SNPs/trait effect from \(X_{i} \rightarrow Y_{p}\) to \(Y_{i} \rightarrow Y_{p}\) MR (i.e. run a MV MR of the form: \(Y_{p} \sim Y_{i} + X_{i}\)).
  • Add script/function which replaces Neale_ID with trait description to main functions.
  • Add status notebook, largely copied from here (https://github.com/rgayler/fa_sim_cal/blob/master/analysis/m_00_status.Rmd).

3 15/09/2021

  • Clean up figures for group meeting presentation Rmd.
  • Delete RData and rds files.
  • MR between partners (partner vs index) Rmd (can take a lot from early July update meeting).
  • MR within same individual Rmd (can take a lot from August update meeting).
  • Compare paths towards outcome in partner Rmd (can take a lot from August update meeting).
  • Rerun het figures and AM MR summary.
  • Add pipeline_overview.Rmd.

3.1 24/09/2021

  • PC analysis
    • Draw a DAG for this, confirm with Zoltan.
  • Delete binary_added.csv file.
  • Remove left body trait, dietary traits, re-add binary traits.
  • In 2 trait model, restrict to only variables with correlation < 0.8 (play with this a bit until we see that traits are really different).
  • Also include X IVs in adjYiYp models in addition to Y IVs.
  • Check which unrelated group was using in PC GWAS.