Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Make reports shareable by default #367

Closed
nebfield opened this issue Sep 2, 2024 · 3 comments · Fixed by #379 or #382
Closed

Make reports shareable by default #367

nebfield opened this issue Sep 2, 2024 · 3 comments · Fixed by #379 or #382
Labels
enhancement New feature or request

Comments

@nebfield
Copy link
Member

nebfield commented Sep 2, 2024

Description of feature

The report.html is so useful but I can’t share it easily because it shows some of the PGS scores with sample IDs in the head of the score data tibble.

We could:

  1. Remove sample ID column from the tibble or
  2. Just delete the tibble (probably safest)
@nebfield nebfield added the enhancement New feature or request label Sep 2, 2024
@bnwolford
Copy link

I believe it depends on the Biobank whether the PGS value without the pseudoynimized ID is considered summary-level information and less subject to data sharing restrictions. The summary plot should be considered safe summary level data enough as long as the x-axis precision and number of markers of the score are such that one cannot easily work backwards possible genotype combinations from the weights file.

@smlmbrt
Copy link
Member

smlmbrt commented Sep 2, 2024

I think we'll just go with option 2 as it avoids the issue altogether. Do you think that lines on top of a distribution is ok for displaying the results of few (#345)? That would have low precision as you suggest.

@bnwolford
Copy link

I think the lines are ok as long as the x-axis has low precision. I could see there technically being an issue if we consider that a summary statistic on less than 5 or 30 people or whatever the minimum is specified in an ethics application. But the histogram is a really great sanity check so I wouldn't want to remove that feature. Perhaps it could just be toggled on if people have issue with it?

@nebfield nebfield linked a pull request Oct 10, 2024 that will close this issue
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
None yet
Development

Successfully merging a pull request may close this issue.

3 participants