CI calculation added for odds ratio

runjin326 commented 2 years ago

Purpose/implementation Section

What scientific question is your analysis addressing?

Add confidence interval calculation for odds ratio in interaction-plots module

What was your approach?

Three columns - standard_error_or, or_ci_lower_bound and or_ci_upper_bound were added to the results column with the following calculation -

      standard_error_or = sqrt(1/mut11 + 1/mut00 + 1/mut10 + 1/mut01),
      or_ci_lower_bound = exp(log(odds_ratio) - 1.96 * standard_error_or),
      or_ci_upper_bound = exp(log(odds_ratio) + 1.96 * standard_error_or)

What GitHub issue does your pull request address?

https://github.com/AlexsLemonade/OpenPBTA-analysis/issues/1203

Directions for reviewers. Tell potential reviewers what kind of feedback you are soliciting.

Which areas should receive a particularly close look?

Please check and see the addition of CI related columns are as wanted.

Is there anything that you want to discuss further?

No.

Is the analysis in a mature enough form that the resulting figure(s) and/or table(s) are ready for review?

Yes.

Results

What types of results are included (e.g., table, figure)?

All the *.tsv files in the results folder are updated with addition of CI related columns.

What is your summary of the results?

Spot checked a couple entries and the numbers make sense.

Reproducibility Checklist

[x] The dependencies required to run the code in this pull request have been added to the project Dockerfile.
[ ] This analysis has been added to continuous integration.

Documentation Checklist

[x] This analysis module has a README and it is up to date.
[ ] This analysis is recorded in the table in analyses/README.md and the entry is up to date.
[x] The analytical code is documented and contains comments.

runjin326 commented 2 years ago

@jashapiro, thanks so much for your prompt review - I would probably take the first approach and ping you for another review when completed.

runjin326 commented 2 years ago

@jashapiro, I pulled out function for CI and now the results only have one ci column with the calculation that you specified. Could you please check to see whether this is what you expect? Thanks!

runjin326 commented 2 years ago

@jashapiro , thanks so much for the detailed review and instructions. I fixed the scripts based on your suggestion - please check to see whether this now looks good.

AlexsLemonade / OpenPBTA-analysis