Use `alt final` instead of phenotype

[runjin326]

Purpose/implementation Section

What scientific question is your analysis addressing?

I think at one point, I asked Jenny and she mentioned that alt_final is the column we should use. Hence, started this PR against re-run 04.

What was your approach?

Modify alt final to all upper case column alt_final - and instead of using phenotype, we use alt_final.

What GitHub issue does your pull request address?

NA

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

Which areas should receive a particularly close look?

Please double check to make sure we want to use alt_final

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)?

Figures:

all-pbta-by-subgroup.pdf    
all-pbta.pdf            
hgat.pdf            
non-hgat.pdf

What is your summary of the results?

The results are consistent with the results when we use phenotype.

Reproducibility Checklist

• [ ] 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

• [ ] 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.
• [ ] The analytical code is documented and contains comments.

[jharenza]

Oh yes, thanks for catching that!