Create list of cancer group/path dx discrepancies based on high-confidence methyl subtypes

[zzgeng]

Purpose/implementation Section

What scientific question is your analysis addressing?

Create a list of samples whose pathology diagnosis and/or finalized molecular subtype & cancer group do not agree with the corresponding high confidence (>= 0.8 methyl score) methylation subtype calls.

What was your approach?

What GitHub issue does your pull request address?

https://github.com/PediatricOpenTargets/ticket-tracker/issues/551

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

Which areas should receive a particularly close look?

analyses/diagnosis_QC

Is there anything that you want to discuss further?

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

Results

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

Table

What is your summary of the results?

There are tables contain:

1. All samples with unmatched molecular_subtype and molecular_subtype_methyl
2. Samples that have different broad histology based on molecular_subtype and molecular_subtype_methyl
3. Samples with high confidence (>= 0.8 methyl score) methylation subtype calls but missing both molecular_subtype and molecular_subtype_methyl

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]

Thanks for starting this @zzgeng! Can you add a readme after your vacation? 😀