Last updated: 2021-03-09

Checks: 2 0

Knit directory: dsc_susierss/

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: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Repository version: 40a70c4

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 40a70c4. 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/

Untracked files:
    Untracked:  data/susie_convergence_problem.rds
    Untracked:  data/susie_convergence_problem6.rds
    Untracked:  data/susierss_ldref.rds

Unstaged changes:
    Modified:   analysis/susierss_ukb_20210218_example.Rmd
    Deleted:    genotype_dir

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/susie_ukb_20210307_convergence.Rmd) and HTML (docs/susie_ukb_20210307_convergence.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 40a70c4 zouyuxin 2021-03-09 wflow_publish(“analysis/susie_ukb_20210307_convergence.Rmd”)
html e4db565 zouyuxin 2021-03-09 Build site.
Rmd 5c02cb4 zouyuxin 2021-03-09 wflow_publish(“analysis/susie_ukb_20210307_convergence.Rmd”)
html cbd5389 zouyuxin 2021-03-09 Build site.
Rmd 5381012 zouyuxin 2021-03-09 wflow_publish(“analysis/susie_ukb_20210307_convergence.Rmd”)
html 444d6fc zouyuxin 2021-03-09 Build site.
Rmd afeef6c zouyuxin 2021-03-09 wflow_publish(“analysis/susie_ukb_20210307_convergence.Rmd”)

This simulation uses UKB genotype data. We extract the genotype regions based on height GWAS result. There are 200 regions, each with 1000 SNPs. We sample 50,000 individuals to simulate the data. We simulate data with 1,2,3 signals and PVE 0.005. We run susie/susie_suff_stat with L=10. We estimate residual and prior variance. We try different initialization, ‘null’ = default initialization; ‘oracle’ = initialize at truth, ‘lasso’ = initialize using LASSO CV solution. We run FINEMAP with oracle number of signals.

Power vs FDR

CS

Overall

1 signal

2 signals

3 signals

ELBO