update pathology free text for LGAT (1/2)

jharenza commented 2 years ago

Purpose/implementation Section

What scientific question is your analysis addressing?

The pathology free text diagnosis subtypes were not being propagated for LGAT

What was your approach?

Removed Notes as a required field for histologies-base.tsv because it was blank and being used in a join, thus missing many samples.
Additionally, I added a substitution for SEGA samples' molecular subtypes to go from LGG, subtype --> SEGA, subtype

What GitHub issue does your pull request address?

The reason behind #1368

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

Which areas should receive a particularly close look?

Is there anything that you want to discuss further?

The few diffs in lines are due to MB WGS samples which were added as To be classified, but the remaining modules were not run since and the HGGs being removed are being removed because of the issue found in https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1382 (were not in classifier results file) but will be updated in https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1383. These HGG samples are subtyped in v21 histologies, but were missed in some of the modules since the runs were not all up to date.

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)?

fixes the LGG subtype propagation issue

What is your summary of the results?

Reproducibility Checklist

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

Documentation Checklist

[x] This analysis module has a README and it is up to date.
[x] 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.

jharenza commented 2 years ago

👍🏻 okay this does not have the issue where some of the fields are NA that I flagged in #1365 and the code changes in analyses/molecular-subtyping-pathology/pathology_free_text-subtyping-lgat.Rmd look fine!

yes, was happy about that and closed that PR as a result

jaclyn-taroni commented 2 years ago

This module was commented out in CI, which no longer seems appropriate!

AlexsLemonade / OpenPBTA-analysis